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16S_QIIME
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# Hunt Creek Salmon 16S 2014-2016
################################
# 1. prep metadata
#Sample List & Mapping Files
Hunt_Creek_Map_R1.txt
#SampleID BarcodeSequence LinkerPrimerSequence Month Day YYYY Date Reach Subreach Source Total_Biofilm_Growth Total_Biofilm_Growth_PostCarcass Year Description
HC.1 TCTCTATGGGATATCT N 10 18 2014 10/18/14 Control I Biofilm 28 14 1 HCUSI18Oct2014BF
HC.2 CGTAGCGAACTATCTG N 10 18 2014 10/18/14 Control II Biofilm 28 14 1 HCUSII18Oct2014BF
HC.3 GCGTATACGACACCGT N 10 18 2014 10/18/14 Control III Biofilm 28 14 1 HCUSIII18Oct2014BF
HC.4 AACGCTGAATCGTACG N 10 3 2014 10/3/14 Control I Biofilm 14 0 1 HCUSI3Oct2014BF
HC.5 TGCTCGTACGTGAGTG N 10 3 2014 10/3/14 Control II Biofilm 14 0 1 HCUSII3Oct2014BF
HC.6 GCGTATACGGATATCT N 10 3 2014 10/3/14 Control III Biofilm 14 0 1 HCUSIII3Oct2014BF
HC.7 CTCGACTTGGATATCT N 10 18 2014 10/18/14 Salmon I Biofilm 28 14 1 HCDSI18Oct2014BF
HC.8 GCGTATACCGTTACTA N 10 18 2014 10/18/14 Salmon II Biofilm 28 14 1 HCDSII18Oct2014BF
HC.9 GCGTATACTACGAGAC N 10 18 2014 10/18/14 Salmon III Biofilm 28 14 1 HCDSIII18Oct2014BF
HC.10 ATAGTACCAGAGTCAC N 10 3 2014 10/3/14 Salmon I Biofilm 14 0 1 HCDSI3Oct2014BF
HC.11 CGAAGTATATCGTACG N 10 3 2014 10/3/14 Salmon II Biofilm 14 0 1 HCDSII3Oct2014BF
HC.12 CGTAGCGACGTTACTA N 10 3 2014 10/3/14 Salmon III Biofilm 14 0 1 HCDSIII3Oct2014BF
Hunt_Creek_Map_R2.txt
#SampleID BarcodeSequence LinkerPrimerSequence Month Day YYYY Date Reach Subreach Source Total_Biofilm_Growth Total_Biofilm_Growth_PostCarcass Year Description
HC.13 GCGTATACCTACTATA N 10 4 2014 10/4/14 Salmon I Carcass 0 0 1 HCDSI4Oct2014C1
HC.14 GCGTATACGTCAGATA N 10 4 2014 10/4/14 Salmon I Carcass 0 0 1 HCDSI4Oct2014C2
HC.15 GCGTATACAGAGTCAC N 10 4 2014 10/4/14 Salmon I Carcass 0 0 1 HCDSI4Oct2014C3
HC.16 GTAACGAGCTACTATA N 10 4 2014 10/4/14 Salmon II Carcass 0 0 1 HCDSII4Oct2014C4
HC.17 TAGCAGCTACTATCTG N 10 4 2014 10/4/14 Salmon II Carcass 0 0 1 HCDSII4Oct2014C5
HC.18 GATCTACGGATCGTGT N 10 4 2014 10/4/14 Salmon II Carcass 0 0 1 HCDSII4Oct2014C6
HC.19 GATCTACGTACGAGAC N 10 4 2014 10/4/14 Salmon III Carcass 0 0 1 HCDSIII4Oct2014C7
HC.20 ATAGTACCTCGACGAG N 10 4 2014 10/4/14 Salmon III Carcass 0 0 1 HCDSIII4Oct2014C8
HC.21 GCGTATACGATCGTGT N 10 4 2014 10/4/14 Salmon III Carcass 0 0 1 HCDSIII4Oct2014C9
Hunt_Creek_Map_R3.txt
#SampleID BarcodeSequence LinkerPrimerSequence Month Day YYYY Date Reach Subreach Source Total_Biofilm_Growth Total_Biofilm_Growth_PostCarcass Year Description
HC.22 GTAACGAGACGTCTCG N 3 12 2015 3/12/15 Salmon III Biofilm 175 161 1 HCBF13
HC.23 GCGTATACACGTCTCG N 3 12 2015 3/12/15 Salmon II Biofilm 175 161 1 HCBF14
HC.24 GTAACGAGTACGAGAC N 3 12 2015 3/12/15 Salmon I Biofilm 175 161 1 HCBF15
HC.25 CGTAGCGATCGACGAG N 3 12 2015 3/12/15 Control III Biofilm 175 161 1 HCBF16
HC.26 GATCTACGGTCAGATA N 3 12 2015 3/12/15 Control II Biofilm 175 161 1 HCBF17
HC.27 ACGTGCGCGATCGTGT N 3 12 2015 3/12/15 Control I Biofilm 175 161 1 HCBF18
HC.28 GTAACGAGCTACTATA N 5 12 2015 5/12/15 Salmon III Biofilm 236 222 1 HCBF19
HC.29 GCGTATACGATCGTGT N 5 12 2015 5/12/15 Salmon II Biofilm 236 222 1 HCBF20
HC.30 ACGTGCGCTACGAGAC N 5 12 2015 5/12/15 Salmon I Biofilm 236 222 1 HCBF21
HC.31 TAGCAGCTAGAGTCAC N 5 12 2015 5/12/15 Control III Biofilm 236 222 1 HCBF22
HC.32 TCTCTATGGTCAGATA N 5 12 2015 5/12/15 Control II Biofilm 236 222 1 HCBF23
HC.33 GTAACGAGGATCGTGT N 5 12 2015 5/12/15 Control I Biofilm 236 222 1 HCBF24
HC.34 ATAGTACCTCGACGAG N 6 23 2015 6/23/15 Salmon III Biofilm 278 264 1 HCBF25
HC.35 TCTCTATGAGAGTCAC N 6 23 2015 6/23/15 Salmon II Biofilm 278 264 1 HCBF26
HC.36 ACGTGCGCAGAGTCAC N 6 23 2015 6/23/15 Salmon I Biofilm 278 264 1 HCBF27
HC.37 CGTAGCGAGATCGTGT N 6 23 2015 6/23/15 Control III Biofilm 278 264 1 HCBF28
HC.38 GATCTACGCTACTATA N 6 23 2015 6/23/15 Control II Biofilm 278 264 1 HCBF29
HC.39 TAGCAGCTGTCAGATA N 6 23 2015 6/23/15 Control I Biofilm 278 264 1 HCBF30
HC.40 TCTCTATGTACGAGAC N 8 4 2015 8/4/15 Salmon III Biofilm 320 306 1 HCBF31
HC.41 AACGCTGAGATCGTGT N 8 4 2015 8/4/15 Salmon II Biofilm 320 306 1 HCBF32
HC.42 CGAAGTATTCGACGAG N 8 4 2015 8/4/15 Salmon I Biofilm 320 306 1 HCBF33
HC.43 CGTAGCGAACGTCTCG N 8 4 2015 8/4/15 Control III Biofilm 320 306 1 HCBF34
HC.44 GCGTATACCTACTATA N 8 4 2015 8/4/15 Control II Biofilm 320 306 1 HCBF35
HC.45 GATCTACGTCGACGAG N 8 4 2015 8/4/15 Control I Biofilm 320 306 1 HCBF36
HC.46 GCGTATACCGTTACTA N 9 5 2014 9/5/14 Salmon NA Rhyacophila 0 0 1 HCI1
HC.47 GATCTACGCGTTACTA N 9 5 2014 9/5/14 Salmon NA Stegopterna 0 0 1 HCI2
HC.48 TGCTCGTAGATCGTGT N 9 5 2014 9/5/14 Salmon NA Baetis 0 0 1 HCI3
HC.49 ACGTGCGCCTACTATA N 3 12 2015 3/12/15 Salmon NA Rhyacophila 0 161 1 HCI4
HC.50 GCGTATACAGAGTCAC N 3 12 2015 3/12/15 Salmon NA Stegopterna 0 161 1 HCI5
HC.51 TGCTCGTAGTCAGATA N 3 12 2015 3/12/15 Salmon NA Baetis 0 161 1 HCI6
HC.52 ACGTGCGCTCGACGAG N 3 12 2015 3/12/15 Control NA Rhyacophila 0 161 1 HCI7
HC.53 GTAACGAGTCGACGAG N 3 12 2015 3/12/15 Control NA Stegopterna 0 161 1 HCI8
HC.54 ATAGTACCTACGAGAC N 3 12 2015 3/12/15 Control NA Baetis 0 161 1 HCI9
HC.55 CGTAGCGATACGAGAC N 6 23 2015 6/23/15 Salmon NA Rhyacophila 0 264 1 HCI10
HC.56 ACGTGCGCACGTCTCG N 6 23 2015 6/23/15 Salmon NA Stegopterna 0 264 1 HCI11
HC.57 AACGCTGACTACTATA N 6 23 2015 6/23/15 Salmon NA Baetis 0 264 1 HCI12
Hunt_Creek_Map_R4.txt
#SampleID BarcodeSequence LinkerPrimerSequence Month Day YYYY Date Reach Subreach Source Total_Biofilm_Growth Total_Biofilm_Growth_PostCarcass Year Description
HC.58 GTCTGCTATAGCGAGT N 10 4 2015 10/4/15 Salmon III Biofilm 14 0 2 HCDSIII4Oct2015BF
HC.59 TAGTCTCCTCATCGAG N 10 4 2015 10/4/15 Salmon II Biofilm 14 0 2 HCDSII4Oct2015BF
HC.60 CGAGCGACGACACCGT N 10 4 2015 10/4/15 Salmon I Biofilm 14 0 2 HCDSI4Oct2015BF
HC.61 TAGTCTCCCTGCGTGT N 10 4 2015 10/4/15 Control III Biofilm 14 0 2 HCUSIII4Oct2015BF
HC.62 TAGTCTCCGGATATCT N 10 4 2015 10/4/15 Control II Biofilm 14 0 2 HCUSII4Oct2015BF
HC.63 TAGTCTCCTAGCGAGT N 10 4 2015 10/4/15 Control I Biofilm 14 0 2 HCUSI4Oct2015BF
HC.64 TGAGTACGCTGCGTGT N 10 25 2015 10/25/15 Salmon III Biofilm 35 16 2 HCDSIII25Oct2015BF
HC.65 CTGCGTAGCGTGAGTG N 10 25 2015 10/25/15 Salmon II Biofilm 35 16 2 HCDSII25Oct2015BF
HC.66 ACGCTACTCTGCGTGT N 10 25 2015 10/25/15 Salmon I Biofilm 35 16 2 HCDSI25Oct2015BF
HC.67 TAGTCTCCCGTGAGTG N 10 25 2015 10/25/15 Control III Biofilm 35 16 2 HCUSIII25Oct2015BF
HC.68 ACTCACTGGGATATCT N 10 25 2015 10/25/15 Control II Biofilm 35 16 2 HCUSII25Oct2015BF
HC.69 ACGCTACTTAGCGAGT N 10 25 2015 10/25/15 Control I Biofilm 35 16 2 HCUSI25Oct2015BF
HC.70 ACGCTACTGGATATCT N 10 9 2015 10/9/15 Salmon I Carcass 0 0 2 C1
HC.71 TGAGTACGTCATCGAG N 10 9 2015 10/9/15 Salmon I Carcass 0 0 2 C3
HC.72 GACATAGTCTGCGTGT N 10 9 2015 10/9/15 Salmon I Carcass 0 0 2 C5
HC.73 CTGCGTAGTCATCGAG N 10 9 2015 10/9/15 Salmon II Carcass 0 0 2 C12
HC.74 TGAGTACGGGATATCT N 10 9 2015 10/9/15 Salmon II Carcass 0 0 2 C13
HC.75 ACTACGACCGTGAGTG N 10 9 2015 10/9/15 Salmon II Carcass 0 0 2 C14
HC.76 CGAGCGACTAGCGAGT N 10 9 2015 10/9/15 Salmon III Carcass 0 0 2 C17
HC.77 CGAGCGACACTATCTG N 10 9 2015 10/9/15 Salmon III Carcass 0 0 2 C18
HC.78 ACTACGACATCGTACG N 10 9 2015 10/9/15 Salmon III Carcass 0 0 2 C19
HC.79 ACTACGACTAGCGAGT N 10 9 2015 10/9/15 Salmon III Carcass 0 0 2 C20
Hunt_Creek_Map_R5.txt
#SampleID BarcodeSequence LinkerPrimerSequence Month Day YYYY Date Reach Subreach Source Total_Biofilm_Growth Total_Biofilm_Growth_PostCarcass Year Description
HC.80 ATAGTACCTACGAGAC N 6 30 2016 6/30/16 Control I Biofilm 279 265 2 HCUSI30June2016BF
HC.81 GTAACGAGTAGCGAGT N 6 30 2016 6/30/16 Control II Biofilm 279 265 2 HCUSII30June2016BF
HC.82 CTCGACTTCGTGAGTG N 6 30 2016 6/30/16 Control III Biofilm 279 265 2 HCUSIII30June2016BF
HC.83 ATAGTACCTCATCGAG N 6 30 2016 6/30/16 Salmon I Biofilm 279 265 2 HCDSI30June2016BF
HC.84 GATCTACGTAGCGAGT N 6 30 2016 6/30/16 Salmon II Biofilm 279 265 2 HCDSII30June2016BF
HC.85 GATCTACGGACACCGT N 6 30 2016 6/30/16 Salmon III Biofilm 279 265 2 HCDSIII30June2016BF
Hunt_Creek_Map_R6.txt
HC.86 CGTAGCGAACGTCTCG N 8 4 2015 8/4/15 Salmon NA Baetis 320 306 1 B
HC.87 GTAACGAGCGTTACTA N 8 4 2015 8/4/15 Salmon NA Baetis 320 306 1 C
HC.88 CGAAGTATAGAGTCAC N 8 4 2015 8/4/15 Control NA Baetis 320 306 1 D
HC.89 TGCTCGTAGTCAGATA N 8 4 2015 8/4/15 Control NA Baetis 320 306 1 E
HC.90 ATAGTACCTACGAGAC N 8 4 2015 8/4/15 Control NA Baetis 320 306 1 F
HC.91 TCTCTATGCTGCGTGT N 3 19 2016 3/19/16 Salmon III Biofilm 176 162 2 HCDSIII19Mar2016BF
HC.92 TAGCAGCTATCGTACG N 3 19 2016 3/19/16 Salmon II Biofilm 176 162 2 HCDSII19Mar2016BF
HC.93 ACGTGCGCTAGCGAGT N 3 19 2016 3/19/16 Salmon I Biofilm 176 162 2 HCDSI19Mar2016BF
HC.94 CGAAGTATATCGTACG N 3 19 2016 3/19/16 Control III Biofilm 176 162 2 HCUSIII19Mar2016BF
HC.95 GTAACGAGCTGCGTGT N 3 19 2016 3/19/16 Control II Biofilm 176 162 2 HCUSII19Mar2016BF
HC.96 CGAAGTATTAGCGAGT N 3 19 2016 3/19/16 Control I Biofilm 176 162 2 HCUSI19Mar2016BF
Hunt_Creek_Map_R7.txt
SampleID BarcodeSequence LinkerPrimerSequence Month Day YYYY Date Reach Subreach Source Total_Biofilm_Growth Total_Biofilm_Growth_PostCarcass Year Description
HC.97 TGCTCGTATGCGTACG N 5 17 2016 5/17/16 Salmon III Biofilm 235 221 2 HCDSIII17May2016BF
HC.98 TGCTCGTAATATACAC N 5 17 2016 5/17/16 Salmon II Biofilm 235 221 2 HCDSII17May2016BF
HC.99 ACGTGCGCCTAGAGCT N 5 17 2016 5/17/16 Salmon I Biofilm 235 221 2 HCDSI17May2016BF
HC.100 ATAGTACCATATACAC N 5 17 2016 5/17/16 Control III Biofilm 235 221 2 HCUSIII17May2016BF
HC.101 TGCTCGTACGTCGCTA N 5 17 2016 5/17/16 Control II Biofilm 235 221 2 HCUSII17May2016BF
HC.102 ATAGTACCCGTCGCTA N 5 17 2016 5/17/16 Control I Biofilm 235 221 2 HCUSI17May2016BF
HC.103 AACGCTGATGCGTACG N 8 15 2016 8/15/16 Salmon III Biofilm 325 311 2 HCDSIII15Aug2016BF
HC.104 CGTAGCGAATATACAC N 8 15 2016 8/15/16 Salmon II Biofilm 325 311 2 HCDSII15Aug2016BF
HC.105 GCGTATACCGTCGCTA N 8 15 2016 8/15/16 Salmon I Biofilm 325 311 2 HCDSI15Aug2016BF
HC.106 GCGTATACTGCGTACG N 8 15 2016 8/15/16 Control III Biofilm 325 311 2 HCUSIII15Aug2016BF
HC.107 AACGCTGAATATACAC N 8 15 2016 8/15/16 Control II Biofilm 325 311 2 HCUSII15Aug2016BF
HC.108 ACGTGCGCGCTCTAGT N 8 15 2016 8/15/16 Control I Biofilm 325 311 2 HCUSI15Aug2016BF
HC.109 TGAGTACGCTAGAGCT N 3 19 2016 3/19/16 Salmon III Baetis 176 162 2 G
HC.110 ACTCACTGACGACGTG N 3 19 2016 3/19/16 Salmon III Baetis 176 162 2 H
HC.111 CGAAGTATGCTCTAGT N 3 19 2016 3/19/16 Salmon II Baetis 176 162 2 I
HC.112 AACGCTGAGCTCTAGT N 6 30 2016 6/30/16 Control I Baetis 279 265 2 J
HC.113 AACGCTGACGTCGCTA N 6 30 2016 6/30/16 Control I Baetis 279 265 2 K
HC.115 CGTAGCGACGTCGCTA N 6 30 2016 6/30/16 Control II Baetis 279 265 2 N
HC.116 TGCTCGTAGCTCTAGT N 6 30 2016 6/30/16 Salmon III Baetis 279 265 2 P
HC.117 AACGCTGAACGACGTG N 6 30 2016 6/30/16 Salmon III Baetis 279 265 2 Q
HC.118 ATAGTACCGACACTGA N 6 30 2016 6/30/16 Salmon III Baetis 279 265 2 R
HC.119 AACGCTGATAGTGTAG N 9 20 2015 9/20/15 Salmon III Baetis 0 352 1 T
HC.120 ATAGTACCGCTCTAGT N 9 20 2015 9/20/15 Control I Baetis 0 352 1 U
HC.121 TATAGCGACGTCGCTA N 5 17 2016 5/17/16 Salmon I Baetis 235 221 2 V
HC.122 GATCTACGATATACAC N 5 17 2016 5/17/16 Salmon I Baetis 235 221 2 W
HC.123 TAGCAGCTCTAGAGCT N 5 17 2016 5/17/16 Salmon II Baetis 235 221 2 X
HC.124 TAGCAGCTATATACAC N 5 17 2016 5/17/16 Salmon II Baetis 235 221 2 Y
HC.125 TCTCTATGACGACGTG N 5 17 2016 5/17/16 Salmon II Baetis 235 221 2 Z
HC.126 TCTCTATGGCTCTAGT N 5 17 2016 5/17/16 Salmon II Baetis 235 221 2 AA
HC.127 GTAACGAGGCTCTAGT N 5 17 2016 5/17/16 Salmon II Baetis 235 221 2 AB
HC.128 TAGCAGCTACGACGTG N 5 17 2016 5/17/16 Salmon III Baetis 235 221 2 AC
HC.129 TCTCTATGGACACTGA N 5 17 2016 5/17/16 Salmon III Baetis 235 221 2 AD
HC.130 TAGCAGCTTAGTGTAG N 5 17 2016 5/17/16 Salmon III Baetis 235 221 2 AE
HC.131 ATAGTACCACGACGTG N 5 17 2016 5/17/16 Salmon III Baetis 235 221 2 AF
HC.132 TAGCAGCTCGTCGCTA N 5 17 2016 5/17/16 Control I Baetis 235 221 2 AG
HC.133 TAGCAGCTGACACTGA N 5 17 2016 5/17/16 Control I Baetis 235 221 2 AH
HC.134 GATCTACGACGACGTG N 5 17 2016 5/17/16 Control I Baetis 235 221 2 AI
HC.135 TCTCTATGCTAGAGCT N 5 17 2016 5/17/16 Control I Baetis 235 221 2 AJ
HC.136 GTAACGAGACGACGTG N 5 17 2016 5/17/16 Control I Baetis 235 221 2 AK
HC.137 GATCTACGCGTCGCTA N 5 17 2016 5/17/16 Control II Baetis 235 221 2 AL
HC.138 TCTCTATGTGCGTACG N 5 17 2016 5/17/16 Control II Baetis 235 221 2 AM
HC.139 GTAACGAGCGTCGCTA N 5 17 2016 5/17/16 Control II Baetis 235 221 2 AN
HC.140 CGAAGTATTGCGTACG N 5 17 2016 5/17/16 Control III Baetis 235 221 2 AO
HC.141 GATCTACGGACACTGA N 5 17 2016 5/17/16 Control III Baetis 235 221 2 AP
HC.142 GCGTATACATATACAC N 5 12 2015 5/12/15 Control III Baetis 222 250 1 AQ
HC.143 AACGCTGAGACACTGA N 5 12 2015 5/12/15 Salmon III Baetis 222 250 1 AR
HC.144 GCGTATACGACACTGA N 5 12 2015 5/12/15 Salmon I Baetis 222 250 1 AS
HC.145 GCGTATACGCTCTAGT N 5 12 2015 5/12/15 Salmon I Baetis 222 250 1 AT
HC.146 AACGCTGACTAGAGCT N 5 12 2015 5/12/15 Salmon I Baetis 222 250 1 AU
HC.147 TGCTCGTATAGTGTAG N 5 12 2015 5/12/15 Salmon I Baetis 222 250 1 AV
HC.148 ACGTGCGCATATACAC N 3 19 2016 3/19/16 Salmon III Stegopterna 176 162 2 A
HC.149 ACGTGCGCACGACGTG N 3 19 2016 3/19/16 Salmon II Stegopterna 176 162 2 B
HC.150 ACGTGCGCTAGTGTAG N 6 30 2016 6/30/16 Control I Simulium 279 265 2 A
HC.151 CGTAGCGAACGACGTG N 6 30 2016 6/30/16 Control I Simulium 279 265 2 B
HC.152 GCGTATACCTAGAGCT N 6 30 2016 6/30/16 Control II Simulium 279 265 2 C
HC.153 TGCTCGTAGACACTGA N 6 30 2016 6/30/16 Salmon III Simulium 279 265 2 D
HC.154 TGCTCGTAACGACGTG N 5 17 2016 5/17/16 Salmon II Stegopterna 235 221 2 HC_I_DS_SRII_17_May_2016_S_26
HC.155 ACGTGCGCGACACTGA N 5 17 2016 5/17/16 Salmon II Stegopterna 235 221 2 HC_I_DS_SRII_17_May_2016_S_27
HC.156 GTAACGAGTGCGTACG N 5 17 2016 5/17/16 Salmon III Stegopterna 235 221 2 HC_I_DS_SRIII_17_May_2016_S_28
HC.157 ATAGTACCTGCGTACG N 5 17 2016 5/17/16 Salmon III Stegopterna 235 221 2 HC_I_DS_SRIII_17_May_2016_S_29
HC.158 ACGTGCGCTGCGTACG N 5 17 2016 5/17/16 Salmon III Stegopterna 235 221 2 HC_I_DS_SRIII_17_May_2016_S_30
HC.159 GTAACGAGTAGTGTAG N 5 17 2016 5/17/16 Control I Stegopterna 235 221 2 HC_I_US_SRI_17_May_2016_S_31
HC.160 GCGTATACTAGTGTAG N 5 17 2016 5/17/16 Control I Stegopterna 235 221 2 HC_I_US_SRI_17_May_2016_S_32
HC.161 TGCTCGTACTAGAGCT N 5 17 2016 5/17/16 Control I Stegopterna 235 221 2 HC_I_US_SRI_17_May_2016_S_33
HC.162 ATAGTACCCTAGAGCT N 5 17 2016 5/17/16 Control II Stegopterna 235 221 2 HC_I_US_SRII_17_May_2016_S_34
HC.163 ATAGTACCTAGTGTAG N 5 17 2016 5/17/16 Control II Stegopterna 235 221 2 HC_I_US_SRII_17_May_2016_S_35
HC.164 GCGTATACACGACGTG N 5 17 2016 5/17/16 Control II Stegopterna 235 221 2 HC_I_US_SRII_17_May_2016_S_36
HC.165 ACGTGCGCCGTCGCTA N 9 5 2014 9/5/14 Control II Stegopterna 0 0 1 HC_I_US_SRII_5_Sep_2014_S_37
HC.166 GTAACGAGCTAGAGCT N 9 5 2014 9/5/14 Control II Stegopterna 0 0 1 HC_I_US_SRII_5_Sep_2014_S_38
HC.167 GATCTACGTGCGTACG N 9 5 2014 9/5/14 Control II Stegopterna 0 0 1 HC_I_US_SRII_5_Sep_2014_S_39
HC.168 TCTCTATGATATACAC N 3 19 2016 3/19/16 Salmon III Stegopterna 176 162 2 HC_I_DS_SRIII_19_Mar_2016_H_40
HC.169 CTGCGTAGACGACGTG N 3 19 2016 3/19/16 Salmon II Heptagenia 176 162 2 HC_I_DS_SRII_19_Mar_2016_H_41
HC.170 GTAACGAGGACACTGA N 3 19 2016 3/19/16 Salmon II Heptagenia 176 162 2 HC_I_DS_SRII_19_Mar_2016_H_42
HC.171 TCTCTATGCGTCGCTA N 3 19 2016 3/19/16 Salmon I Heptagenia 176 162 2 HC_I_DS_SRI_19_Mar_2016_H_43
HC.172 ACTACGACCGTCGCTA N 5 17 2016 5/17/16 Salmon I Heptagenia 235 221 2 HC_I_DS_SRI_17_May_2016_H_44
HC.173 CGAGCGACTGCGTACG N 5 17 2016 5/17/16 Salmon I Heptagenia 235 221 2 HC_I_DS_SRI_17_May_2016_H_45
HC.174 GTCTGCTACTAGAGCT N 5 17 2016 5/17/16 Salmon I Heptagenia 235 221 2 HC_I_DS_SRI_17_May_2016_H_46
HC.175 GATCTACGGCTCTAGT N 5 17 2016 5/17/16 Salmon I Heptagenia 235 221 2 HC_I_DS_SRI_17_May_2016_H_47
HC.176 CGAAGTATGACACTGA N 5 17 2016 5/17/16 Salmon II Heptagenia 235 221 2 HC_I_DS_SRII_17_May_2016_H_48
#Sequence Reads
HC_1_AACGCTGA-ATCGTACG_L001_R2_001.fastq
HC_1_AACGCTGA-ATCGTACG_L001_R2_001.fastq
HC_2_TGCTCGTA-CGTGAGTG_L001_R1_001.fastq
HC_2_TGCTCGTA-CGTGAGTG_L001_R2_001.fastq
HC_3_GCGTATAC-GGATATCT_L001_R1_001.fastq
HC_3_GCGTATAC-GGATATCT_L001_R2_001.fastq
HC_4_ATAGTACC-AGAGTCAC_L001_R1_001.fastq
HC_4_ATAGTACC-AGAGTCAC_L001_R2_001.fastq
HC_5_CGAAGTAT-ATCGTACG_L001_R1_001.fastq
HC_5_CGAAGTAT-ATCGTACG_L001_R2_001.fastq
HC_6_CGTAGCGA-CGTTACTA_L001_R1_001.fastq
HC_6_CGTAGCGA-CGTTACTA_L001_R2_001.fastq
HC_7_TCTCTATG-GGATATCT_L001_R1_001.fastq
HC_7_TCTCTATG-GGATATCT_L001_R2_001.fastq
HC_8_CGTAGCGA-ACTATCTG_L001_R1_001.fastq
HC_8_CGTAGCGA-ACTATCTG_L001_R2_001.fastq
HC_9_GCGTATAC-GACACCGT_L001_R1_001.fastq
HC_9_GCGTATAC-GACACCGT_L001_R2_001.fastq
HC_10_CTCGACT-TGGATATCT_L001_R1_001.fastq
HC_10_CTCGACT-TGGATATCT_L001_R2_001.fastq
HC_11_GCGTATA-CCGTTACTA_L001_R1_001.fastq
HC_11_GCGTATA-CCGTTACTA_L001_R2_001.fastq
HC_12_GCGTATA-CTACGAGAC_L001_R1_001.fastq
HC_12_GCGTATA-CTACGAGAC_L001_R2_001.fastq
HC_13_GCGTATAC-CTACTATA_L001_R1_001.fastq
HC_13_GCGTATAC-CTACTATA_L001_R2_001.fastq
HC_14_GCGTATAC-GTCAGATA_L001_R1_001.fastq
HC_14_GCGTATAC-GTCAGATA_L001_R2_001.fastq
HC_15_GCGTATAC-AGAGTCAC_L001_R1_001.fastq
HC_15_GCGTATAC-AGAGTCAC_L001_R2_001.fastq
HC_16_GTAACGAG-CTACTATA_L001_R1_001.fastq
HC_16_GTAACGAG-CTACTATA_L001_R2_001.fastq
HC_17_TAGCAGCT-ACTATCTG_L001_R1_001.fastq
HC_17_TAGCAGCT-ACTATCTG_L001_R2_001.fastq
HC_18_GATCTACG-GATCGTGT_L001_R1_001.fastq
HC_18_GATCTACG-GATCGTGT_L001_R2_001.fastq
HC_19_GATCTACG-TACGAGAC_L001_R1_001.fastq
HC_19_GATCTACG-TACGAGAC_L001_R2_001.fastq
HC_20_ATAGTACC-TCGACGAG_L001_R1_001.fastq
HC_20_ATAGTACC-TCGACGAG_L001_R2_001.fastq
HC_21_GCGTATAC-GATCGTGT_L001_R1_001.fastq
HC_21_GCGTATAC-GATCGTGT_L001_R2_001.fastq
HC_22_GTAACGAG-ACGTCTCG_L001_R1_001.fastq
HC_22_GTAACGAG-ACGTCTCG_L001_R2_001.fastq
HC_23_GCGTATAC-ACGTCTCG_L001_R1_001.fastq
HC_23_GCGTATAC-ACGTCTCG_L001_R2_001.fastq
HC_24_GTAACGAG-TACGAGAC_L001_R1_001.fastq
HC_24_GTAACGAG-TACGAGAC_L001_R2_001.fastq
HC_25_CGTAGCGA-TCGACGAG_L001_R1_001.fastq
HC_25_CGTAGCGA-TCGACGAG_L001_R2_001.fastq
HC_26_GATCTACG-GTCAGATA_L001_R1_001.fastq
HC_26_GATCTACG-GTCAGATA_L001_R2_001.fastq
HC_27_ACGTGCGC-GATCGTGT_L001_R1_001.fastq
HC_27_ACGTGCGC-GATCGTGT_L001_R2_001.fastq
HC_28_GTAACGAG-CTACTATA_L001_R1_001.fastq
HC_28_GTAACGAG-CTACTATA_L001_R2_001.fastq
HC_29_GCGTATAC-GATCGTGT_L001_R1_001.fastq
HC_29_GCGTATAC-GATCGTGT_L001_R2_001.fastq
HC_30_ACGTGCGC-TACGAGAC_L001_R1_001.fastq
HC_30_ACGTGCGC-TACGAGAC_L001_R2_001.fastq
HC_31_TAGCAGCT-AGAGTCAC_L001_R1_001.fastq
HC_31_TAGCAGCT-AGAGTCAC_L001_R2_001.fastq
HC_32_TCTCTATG-GTCAGATA_L001_R1_001.fastq
HC_32_TCTCTATG-GTCAGATA_L001_R2_001.fastq
HC_33_GTAACGAG-GATCGTGT_L001_R1_001.fastq
HC_33_GTAACGAG-GATCGTGT_L001_R2_001.fastq
HC_34_ATAGTACC-TCGACGAG_L001_R1_001.fastq
HC_34_ATAGTACC-TCGACGAG_L001_R2_001.fastq
HC_35_TCTCTATG-AGAGTCAC_L001_R1_001.fastq
HC_35_TCTCTATG-AGAGTCAC_L001_R2_001.fastq
HC_36_ACGTGCGC-AGAGTCAC_L001_R1_001.fastq
HC_36_ACGTGCGC-AGAGTCAC_L001_R2_001.fastq
HC_37_CGTAGCGA-GATCGTGT_L001_R1_001.fastq
HC_37_CGTAGCGA-GATCGTGT_L001_R2_001.fastq
HC_38_GATCTACG-CTACTATA_L001_R1_001.fastq
HC_38_GATCTACG-CTACTATA_L001_R2_001.fastq
HC_39_TAGCAGCT-GTCAGATA_L001_R1_001.fastq
HC_39_TAGCAGCT-GTCAGATA_L001_R2_001.fastq
HC_40_TCTCTATG-TACGAGAC_L001_R1_001.fastq
HC_40_TCTCTATG-TACGAGAC_L001_R2_001.fastq
HC_41_AACGCTGA-GATCGTGT_L001_R1_001.fastq
HC_41_AACGCTGA-GATCGTGT_L001_R2_001.fastq
HC_42_CGAAGTAT-TCGACGAG_L001_R1_001.fastq
HC_42_CGAAGTAT-TCGACGAG_L001_R2_001.fastq
HC_43_CGTAGCGA-ACGTCTCG_L001_R1_001.fastq
HC_43_CGTAGCGA-ACGTCTCG_L001_R2_001.fastq
HC_44_GCGTATAC-CTACTATA_L001_R1_001.fastq
HC_44_GCGTATAC-CTACTATA_L001_R2_001.fastq
HC_45_GATCTACG-TCGACGAG_L001_R1_001.fastq
HC_45_GATCTACG-TCGACGAG_L001_R2_001.fastq
HC_46_GCGTATAC-CGTTACTA_L001_R1_001.fastq
HC_46_GCGTATAC-CGTTACTA_L001_R2_001.fastq
HC_47_GATCTACG-CGTTACTA_L001_R1_001.fastq
HC_47_GATCTACG-CGTTACTA_L001_R2_001.fastq
HC_48_TGCTCGTA-GATCGTGT_L001_R1_001.fastq
HC_48_TGCTCGTA-GATCGTGT_L001_R2_001.fastq
HC_49_ACGTGCGC-CTACTATA_L001_R1_001.fastq
HC_49_ACGTGCGC-CTACTATA_L001_R2_001.fastq
HC_50_GCGTATAC-AGAGTCAC_L001_R1_001.fastq
HC_50_GCGTATAC-AGAGTCAC_L001_R2_001.fastq
HC_51_TGCTCGTA-GTCAGATA_L001_R1_001.fastq
HC_51_TGCTCGTA-GTCAGATA_L001_R2_001.fastq
HC_52_ACGTGCGC-TCGACGAG_L001_R1_001.fastq
HC_52_ACGTGCGC-TCGACGAG_L001_R2_001.fastq
HC_53_GTAACGAG-TCGACGAG_L001_R1_001.fastq
HC_53_GTAACGAG-TCGACGAG_L001_R2_001.fastq
HC_54_ATAGTACC-TACGAGAC_L001_R1_001.fastq
HC_54_ATAGTACC-TACGAGAC_L001_R2_001.fastq
HC_55_CGTAGCGA-TACGAGAC_L001_R1_001.fastq
HC_55_CGTAGCGA-TACGAGAC_L001_R2_001.fastq
HC_56_ACGTGCGC-ACGTCTCG_L001_R1_001.fastq
HC_56_ACGTGCGC-ACGTCTCG_L001_R2_001.fastq
HC_57_AACGCTGA-CTACTATA_L001_R1_001.fastq
HC_57_AACGCTGA-CTACTATA_L001_R2_001.fastq
HC_58_GTCTGCTA-TAGCGAGT_L001_R1_001.fastq
HC_58_GTCTGCTA-TAGCGAGT_L001_R2_001.fastq
HC_59_TAGTCTCC-TCATCGAG_L001_R1_001.fastq
HC_59_TAGTCTCC-TCATCGAG_L001_R2_001.fastq
HC_60_CGAGCGAC-GACACCGT_L001_R1_001.fastq
HC_60_CGAGCGAC-GACACCGT_L001_R2_001.fastq
HC_61_TAGTCTCC-CTGCGTGT_L001_R1_001.fastq
HC_61_TAGTCTCC-CTGCGTGT_L001_R2_001.fastq
HC_62_TAGTCTCC-GGATATCT_L001_R1_001.fastq
HC_62_TAGTCTCC-GGATATCT_L001_R2_001.fastq
HC_63_TAGTCTCC-TAGCGAGT_L001_R1_001.fastq
HC_63_TAGTCTCC-TAGCGAGT_L001_R2_001.fastq
HC_64_TGAGTACG-CTGCGTGT_L001_R1_001.fastq
HC_64_TGAGTACG-CTGCGTGT_L001_R2_001.fastq
HC_65_CTGCGTAG-CGTGAGTG_L001_R1_001.fastq
HC_65_CTGCGTAG-CGTGAGTG_L001_R2_001.fastq
HC_66_ACGCTACT-CTGCGTGT_L001_R1_001.fastq
HC_66_ACGCTACT-CTGCGTGT_L001_R2_001.fastq
HC_67_TAGTCTCC-CGTGAGTG_L001_R1_001.fastq
HC_67_TAGTCTCC-CGTGAGTG_L001_R2_001.fastq
HC_68_ACTCACTG-GGATATCT_L001_R1_001.fastq
HC_68_ACTCACTG-GGATATCT_L001_R2_001.fastq
HC_69_ACGCTACT-TAGCGAGT_L001_R1_001.fastq
HC_69_ACGCTACT-TAGCGAGT_L001_R2_001.fastq
HC_70_ACGCTACT-GGATATCT_L001_R1_001.fastq
HC_70_ACGCTACT-GGATATCT_L001_R2_001.fastq
HC_71_TGAGTACG-TCATCGAG_L001_R1_001.fastq
HC_71_TGAGTACG-TCATCGAG_L001_R2_001.fastq
HC_72_GACATAGT-CTGCGTGT_L001_R1_001.fastq
HC_72_GACATAGT-CTGCGTGT_L001_R2_001.fastq
HC_73_CTGCGTAG-TCATCGAG_L001_R1_001.fastq
HC_73_CTGCGTAG-TCATCGAG_L001_R2_001.fastq
HC_74_TGAGTACG-GGATATCT_L001_R1_001.fastq
HC_74_TGAGTACG-GGATATCT_L001_R2_001.fastq
HC_75_ACTACGAC-CGTGAGTG_L001_R1_001.fastq
HC_75_ACTACGAC-CGTGAGTG_L001_R2_001.fastq
HC_76_CGAGCGAC-TAGCGAGT_L001_R1_001.fastq
HC_76_CGAGCGAC-TAGCGAGT_L001_R2_001.fastq
HC_77_CGAGCGAC-ACTATCTG_L001_R1_001.fastq
HC_77_CGAGCGAC-ACTATCTG_L001_R2_001.fastq
HC_78_ACTACGAC-ATCGTACG_L001_R1_001.fastq
HC_78_ACTACGAC-ATCGTACG_L001_R2_001.fastq
HC_79_ACTACGAC-TAGCGAGT_L001_R1_001.fastq
HC_79_ACTACGAC-TAGCGAGT_L001_R2_001.fastq
HuntCr80_S87_L001_R1_001.fastq
HuntCr80_S87_L001_R2_001.fastq
HuntCr81_S60_L001_R1_001.fastq
HuntCr81_S60_L001_R2_001.fastq
HuntCr82_S122_L001_R1_001.fastq
HuntCr82_S122_L001_R2_001.fastq
HuntCr83_S112_L001_R1_001.fastq
HuntCr83_S112_L001_R2_001.fastq
HuntCr84_S58_L001_R1_001.fastq
HuntCr84_S58_L001_R2_001.fastq
HuntCr85_S178_L001_R1_001.fastq
HuntCr85_S178_L001_R2_001.fastq
HuntCr86_S119_L001_R1_001.fastq
HuntCr86_S119_L001_R2_001.fastq
HuntCr87_S35_L001_R1_001.fastq
HuntCr87_S35_L001_R2_001.fastq
HuntCr88_S51_L001_R1_001.fastq
HuntCr88_S51_L001_R2_001.fastq
HuntCr89_S187_L001_R1_001.fastq
HuntCr89_S187_L001_R2_001.fastq
HuntCr90_S137_L001_R1_001.fastq
HuntCr90_S137_L001_R2_001.fastq
HuntCr91_S80_L001_R1_001.fastq
HuntCr91_S80_L001_R2_001.fastq
HuntCr92_S6_L001_R1_001.fastq
HuntCr92_S6_L001_R2_001.fastq
HuntCr93_S62_L001_R1_001.fastq
HuntCr93_S62_L001_R2_001.fastq
HuntCr94_S4_L001_R1_001.fastq
HuntCr94_S4_L001_R2_001.fastq
HuntCr95_S84_L001_R1_001.fastq
HuntCr95_S84_L001_R2_001.fastq
HuntCr96_S52_L001_R1_001.fastq
HuntCr96_S52_L001_R2_001.fastq
HuntCr97_S164_L001_R1_001.fastq
HuntCr97_S164_L001_R2_001.fastq
HuntCr98_S44_L001_R1_001.fastq
HuntCr98_S44_L001_R2_001.fastq
HuntCr99_S86_L001_R1_001.fastq
HuntCr99_S86_L001_R2_001.fastq
HuntCr100_S40_L001_R1_001.fastq
HuntCr100_S40_L001_R2_001.fastq
HuntCr101_S68_L001_R1_001.fastq
HuntCr101_S68_L001_R2_001.fastq
HuntCr102_S64_L001_R1_001.fastq
HuntCr102_S64_L001_R2_001.fastq
HuntCr103_S166_L001_R1_001.fastq
HuntCr103_S166_L001_R2_001.fastq
HuntCr104_S48_L001_R1_001.fastq
HuntCr104_S48_L001_R2_001.fastq
HuntCr105_S66_L001_R1_001.fastq
HuntCr105_S66_L001_R2_001.fastq
HuntCr106_S162_L001_R1_001.fastq
HuntCr106_S162_L001_R2_001.fastq
HuntCr107_S46_L001_R1_001.fastq
HuntCr107_S46_L001_R2_001.fastq
HuntCr108_S110_L001_R1_001.fastq
HuntCr108_S110_L001_R2_001.fastq
HuntCr109_S81_L001_R1_001.fastq
HuntCr109_S81_L001_R2_001.fastq
HuntCr110_S7_L001_R1_001.fastq
HuntCr110_S7_L001_R2_001.fastq
HuntCr111_S100_L001_R1_001.fastq
HuntCr111_S100_L001_R2_001.fastq
HuntCr112_S118_L001_R1_001.fastq
HuntCr112_S118_L001_R2_001.fastq
HuntCr113_S70_L001_R1_001.fastq
HuntCr113_S70_L001_R2_001.fastq
HuntCr115_S72_L001_R1_001.fastq
HuntCr115_S72_L001_R2_001.fastq
HuntCr116_S116_L001_R1_001.fastq
HuntCr116_S116_L001_R2_001.fastq
HuntCr117_S22_L001_R1_001.fastq
HuntCr117_S22_L001_R2_001.fastq
HuntCr118_S136_L001_R1_001.fastq
HuntCr118_S136_L001_R2_001.fastq
HuntCr119_S190_L001_R1_001.fastq
HuntCr119_S190_L001_R2_001.fastq
HuntCr120_S112_L001_R1_001.fastq
HuntCr120_S112_L001_R2_001.fastq
HuntCr121_S71_L001_R1_001.fastq
HuntCr121_S71_L001_R2_001.fastq
HuntCr122_S34_L001_R1_001.fastq
HuntCr122_S34_L001_R2_001.fastq
HuntCr123_S78_L001_R1_001.fastq
HuntCr123_S78_L001_R2_001.fastq
HuntCr124_S30_L001_R1_001.fastq
HuntCr124_S30_L001_R2_001.fastq
HuntCr125_S8_L001_R1_001.fastq
HuntCr125_S8_L001_R2_001.fastq
HuntCr126_S104_L001_R1_001.fastq
HuntCr126_S104_L001_R2_001.fastq
HuntCr127_S108_L001_R1_001.fastq
HuntCr127_S108_L001_R2_001.fastq
HuntCr128_S6_L001_R1_001.fastq
HuntCr128_S6_L001_R2_001.fastq
HuntCr129_S128_L001_R1_001.fastq
HuntCr129_S128_L001_R2_001.fastq
HuntCr130_S174_L001_R1_001.fastq
HuntCr130_S174_L001_R2_001.fastq
HuntCr131_S16_L001_R1_001.fastq
HuntCr131_S16_L001_R2_001.fastq
HuntCr132_S54_L001_R1_001.fastq
HuntCr132_S54_L001_R2_001.fastq
HuntCr133_S126_L001_R1_001.fastq
HuntCr133_S126_L001_R2_001.fastq
HuntCr134_S10_L001_R1_001.fastq
HuntCr134_S10_L001_R2_001.fastq
HuntCr135_S80_L001_R1_001.fastq
HuntCr135_S80_L001_R2_001.fastq
HuntCr136_S12_L001_R1_001.fastq
HuntCr136_S12_L001_R2_001.fastq
HuntCr137_S58_L001_R1_001.fastq
HuntCr137_S58_L001_R2_001.fastq
HuntCr138_S152_L001_R1_001.fastq
HuntCr138_S152_L001_R2_001.fastq
HuntCr139_S60_L001_R1_001.fastq
HuntCr139_S60_L001_R2_001.fastq
HuntCr140_S148_L001_R1_001.fastq
HuntCr140_S148_L001_R2_001.fastq
HuntCr141_S130_L001_R1_001.fastq
HuntCr141_S130_L001_R2_001.fastq
HuntCr142_S42_L001_R1_001.fastq
HuntCr142_S42_L001_R2_001.fastq
HuntCr143_S142_L001_R1_001.fastq
HuntCr143_S142_L001_R2_001.fastq
HuntCr144_S138_L001_R1_001.fastq
HuntCr144_S138_L001_R2_001.fastq
HuntCr145_S114_L001_R1_001.fastq
HuntCr145_S114_L001_R2_001.fastq
HuntCr146_S94_L001_R1_001.fastq
HuntCr146_S94_L001_R2_001.fastq
HuntCr147_S188_L001_R1_001.fastq
HuntCr147_S188_L001_R2_001.fastq
HuntCr148_S38_L001_R1_001.fastq
HuntCr148_S38_L001_R2_001.fastq
HuntCr149_S14_L001_R1_001.fastq
HuntCr149_S14_L001_R2_001.fastq
HuntCr150_S182_L001_R1_001.fastq
HuntCr150_S182_L001_R2_001.fastq
HuntCr151_S24_L001_R1_001.fastq
HuntCr151_S24_L001_R2_001.fastq
HuntCr152_S90_L001_R1_001.fastq
HuntCr152_S90_L001_R2_001.fastq
HuntCr153_S140_L001_R1_001.fastq
HuntCr153_S140_L001_R2_001.fastq
HuntCr154_S20_L001_R1_001.fastq
HuntCr154_S20_L001_R2_001.fastq
HuntCr155_S134_L001_R1_001.fastq
HuntCr155_S134_L001_R2_001.fastq
HuntCr156_S156_L001_R1_001.fastq
HuntCr156_S156_L001_R2_001.fastq
HuntCr157_S160_L001_R1_001.fastq
HuntCr157_S160_L001_R2_001.fastq
HuntCr158_S158_L001_R1_001.fastq
HuntCr158_S158_L001_R2_001.fastq
HuntCr159_S180_L001_R1_001.fastq
HuntCr159_S180_L001_R2_001.fastq
HuntCr160_S186_L001_R1_001.fastq
HuntCr160_S186_L001_R2_001.fastq
HuntCr161_S92_L001_R1_001.fastq
HuntCr161_S92_L001_R2_001.fastq
HuntCr162_S88_L001_R1_001.fastq
HuntCr162_S88_L001_R2_001.fastq
HuntCr163_S184_L001_R1_001.fastq
HuntCr163_S184_L001_R2_001.fastq
HuntCr164_S18_L001_R1_001.fastq
HuntCr164_S18_L001_R2_001.fastq
HuntCr165_S62_L001_R1_001.fastq
HuntCr165_S62_L001_R2_001.fastq
HuntCr166_S84_L001_R1_001.fastq
HuntCr166_S84_L001_R2_001.fastq
HuntCr167_S154_L001_R1_001.fastq
HuntCr167_S154_L001_R2_001.fastq
HuntCr168_S32_L001_R1_001.fastq
HuntCr168_S32_L001_R2_001.fastq
HuntCr169_S11_L001_R1_001.fastq
HuntCr169_S11_L001_R2_001.fastq
HuntCr170_S132_L001_R1_001.fastq
HuntCr170_S132_L001_R2_001.fastq
HuntCr171_S56_L001_R1_001.fastq
HuntCr171_S56_L001_R2_001.fastq
HuntCr172_S65_L001_R1_001.fastq
HuntCr172_S65_L001_R2_001.fastq
HuntCr173_S159_L001_R1_001.fastq
HuntCr173_S159_L001_R2_001.fastq
HuntCr174_S91_L001_R1_001.fastq
HuntCr174_S91_L001_R2_001.fastq
HuntCr175_S106_L001_R1_001.fastq
HuntCr175_S106_L001_R2_001.fastq
HuntCr176_S124_L001_R1_001.fastq
HuntCr176_S124_L001_R2_001.fastq
################################
# 2. join paired ends for each sample (individually)
# cd to Desktop folder named "Core"
cd ~/Desktop/Core/16S/
# join_paired_ends.py -f $PWD/forward_reads.fastq -r $PWD/reverse_reads.fastq -o $PWD/fastq-join_joined
join_paired_ends.py -f HC_1_AACGCTGA-ATCGTACG_L001_R1_001.fastq -r HC_1_AACGCTGA-ATCGTACG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_1
join_paired_ends.py -f HC_2_TGCTCGTA-CGTGAGTG_L001_R1_001.fastq -r HC_2_TGCTCGTA-CGTGAGTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_2
join_paired_ends.py -f HC_3_GCGTATAC-GGATATCT_L001_R1_001.fastq -r HC_3_GCGTATAC-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_3
join_paired_ends.py -f HC_4_ATAGTACC-AGAGTCAC_L001_R1_001.fastq -r HC_4_ATAGTACC-AGAGTCAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_4
join_paired_ends.py -f HC_5_CGAAGTAT-ATCGTACG_L001_R1_001.fastq -r HC_5_CGAAGTAT-ATCGTACG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_5
join_paired_ends.py -f HC_6_CGTAGCGA-CGTTACTA_L001_R1_001.fastq -r HC_6_CGTAGCGA-CGTTACTA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_6
join_paired_ends.py -f HC_7_TCTCTATG-GGATATCT_L001_R1_001.fastq -r HC_7_TCTCTATG-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_7
join_paired_ends.py -f HC_8_CGTAGCGA-ACTATCTG_L001_R1_001.fastq -r HC_8_CGTAGCGA-ACTATCTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_8
join_paired_ends.py -f HC_9_GCGTATAC-GACACCGT_L001_R1_001.fastq -r HC_9_GCGTATAC-GACACCGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_9
join_paired_ends.py -f HC_10_CTCGACTT-GGATATCT_L001_R1_001.fastq -r HC_10_CTCGACTT-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_10
join_paired_ends.py -f HC_11_GCGTATAC-CGTTACTA_L001_R1_001.fastq -r HC_11_GCGTATAC-CGTTACTA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_11
join_paired_ends.py -f HC_12_GCGTATAC-TACGAGAC_L001_R1_001.fastq -r HC_12_GCGTATAC-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_12
join_paired_ends.py -f HC_13_GCGTATAC-CTACTATA_L001_R1_001.fastq -r HC_13_GCGTATAC-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_13
join_paired_ends.py -f HC_14_GCGTATAC-GTCAGATA_L001_R1_001.fastq -r HC_14_GCGTATAC-GTCAGATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_14
join_paired_ends.py -f HC_15_GCGTATAC-AGAGTCAC_L001_R1_001.fastq -r HC_15_GCGTATAC-AGAGTCAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_15
join_paired_ends.py -f HC_16_GTAACGAG-CTACTATA_L001_R1_001.fastq -r HC_16_GTAACGAG-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_16
join_paired_ends.py -f HC_17_TAGCAGCT-ACTATCTG_L001_R1_001.fastq -r HC_17_TAGCAGCT-ACTATCTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_17
join_paired_ends.py -f HC_18_GATCTACG-GATCGTGT_L001_R1_001.fastq -r HC_18_GATCTACG-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_18
join_paired_ends.py -f HC_19_GATCTACG-TACGAGAC_L001_R1_001.fastq -r HC_19_GATCTACG-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_19
join_paired_ends.py -f HC_20_ATAGTACC-TCGACGAG_L001_R1_001.fastq -r HC_20_ATAGTACC-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_20
join_paired_ends.py -f HC_21_GCGTATAC-GATCGTGT_L001_R1_001.fastq -r HC_21_GCGTATAC-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_21
join_paired_ends.py -f HC_22_GTAACGAG-ACGTCTCG_L001_R1_001.fastq -r HC_22_GTAACGAG-ACGTCTCG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_22
join_paired_ends.py -f HC_23_GCGTATAC-ACGTCTCG_L001_R1_001.fastq -r HC_23_GCGTATAC-ACGTCTCG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_23
join_paired_ends.py -f HC_24_GTAACGAG-TACGAGAC_L001_R1_001.fastq -r HC_24_GTAACGAG-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_24
join_paired_ends.py -f HC_25_CGTAGCGA-TCGACGAG_L001_R1_001.fastq -r HC_25_CGTAGCGA-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_25
join_paired_ends.py -f HC_26_GATCTACG-GTCAGATA_L001_R1_001.fastq -r HC_26_GATCTACG-GTCAGATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_26
join_paired_ends.py -f HC_27_ACGTGCGC-GATCGTGT_L001_R1_001.fastq -r HC_27_ACGTGCGC-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_27
join_paired_ends.py -f HC_28_GTAACGAG-CTACTATA_L001_R1_001.fastq -r HC_28_GTAACGAG-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_28
join_paired_ends.py -f HC_29_GCGTATAC-GATCGTGT_L001_R1_001.fastq -r HC_29_GCGTATAC-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_29
join_paired_ends.py -f HC_30_ACGTGCGC-TACGAGAC_L001_R1_001.fastq -r HC_30_ACGTGCGC-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_30
join_paired_ends.py -f HC_31_TAGCAGCT-AGAGTCAC_L001_R1_001.fastq -r HC_31_TAGCAGCT-AGAGTCAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_31
join_paired_ends.py -f HC_32_TCTCTATG-GTCAGATA_L001_R1_001.fastq -r HC_32_TCTCTATG-GTCAGATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_32
join_paired_ends.py -f HC_33_GTAACGAG-GATCGTGT_L001_R1_001.fastq -r HC_33_GTAACGAG-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_33
join_paired_ends.py -f HC_34_ATAGTACC-TCGACGAG_L001_R1_001.fastq -r HC_34_ATAGTACC-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_34
join_paired_ends.py -f HC_35_TCTCTATG-AGAGTCAC_L001_R1_001.fastq -r HC_35_TCTCTATG-AGAGTCAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_35
join_paired_ends.py -f HC_36_ACGTGCGC-AGAGTCAC_L001_R1_001.fastq -r HC_36_ACGTGCGC-AGAGTCAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_36
join_paired_ends.py -f HC_37_CGTAGCGA-GATCGTGT_L001_R1_001.fastq -r HC_37_CGTAGCGA-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_37
join_paired_ends.py -f HC_38_GATCTACG-CTACTATA_L001_R1_001.fastq -r HC_38_GATCTACG-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_38
join_paired_ends.py -f HC_39_TAGCAGCT-GTCAGATA_L001_R1_001.fastq -r HC_39_TAGCAGCT-GTCAGATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_39
join_paired_ends.py -f HC_40_TCTCTATG-TACGAGAC_L001_R1_001.fastq -r HC_40_TCTCTATG-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_40
join_paired_ends.py -f HC_41_AACGCTGA-GATCGTGT_L001_R1_001.fastq -r HC_41_AACGCTGA-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_41
join_paired_ends.py -f HC_42_CGAAGTAT-TCGACGAG_L001_R1_001.fastq -r HC_42_CGAAGTAT-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_42
join_paired_ends.py -f HC_43_CGTAGCGA-ACGTCTCG_L001_R1_001.fastq -r HC_43_CGTAGCGA-ACGTCTCG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_43
join_paired_ends.py -f HC_44_GCGTATAC-CTACTATA_L001_R1_001.fastq -r HC_44_GCGTATAC-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_44
join_paired_ends.py -f HC_45_GATCTACG-TCGACGAG_L001_R1_001.fastq -r HC_45_GATCTACG-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_45
join_paired_ends.py -f HC_46_GCGTATAC-CGTTACTA_L001_R1_001.fastq -r HC_46_GCGTATAC-CGTTACTA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_46
join_paired_ends.py -f HC_47_GATCTACG-CGTTACTA_L001_R1_001.fastq -r HC_47_GATCTACG-CGTTACTA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_47
join_paired_ends.py -f HC_48_TGCTCGTA-GATCGTGT_L001_R1_001.fastq -r HC_48_TGCTCGTA-GATCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_48
join_paired_ends.py -f HC_49_ACGTGCGC-CTACTATA_L001_R1_001.fastq -r HC_49_ACGTGCGC-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_49
join_paired_ends.py -f HC_50_GCGTATAC-AGAGTCAC_L001_R1_001.fastq -r HC_50_GCGTATAC-AGAGTCAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_50
join_paired_ends.py -f HC_51_TGCTCGTA-GTCAGATA_L001_R1_001.fastq -r HC_51_TGCTCGTA-GTCAGATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_51
join_paired_ends.py -f HC_52_ACGTGCGC-TCGACGAG_L001_R1_001.fastq -r HC_52_ACGTGCGC-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_52
join_paired_ends.py -f HC_53_GTAACGAG-TCGACGAG_L001_R1_001.fastq -r HC_53_GTAACGAG-TCGACGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_53
join_paired_ends.py -f HC_54_ATAGTACC-TACGAGAC_L001_R1_001.fastq -r HC_54_ATAGTACC-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_54
join_paired_ends.py -f HC_55_CGTAGCGA-TACGAGAC_L001_R1_001.fastq -r HC_55_CGTAGCGA-TACGAGAC_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_55
join_paired_ends.py -f HC_56_ACGTGCGC-ACGTCTCG_L001_R1_001.fastq -r HC_56_ACGTGCGC-ACGTCTCG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_56
join_paired_ends.py -f HC_57_AACGCTGA-CTACTATA_L001_R1_001.fastq -r HC_57_AACGCTGA-CTACTATA_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_57
join_paired_ends.py -f HC_58_GTCTGCTA-TAGCGAGT_L001_R1_001.fastq -r HC_58_GTCTGCTA-TAGCGAGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_58
join_paired_ends.py -f HC_59_TAGTCTCC-TCATCGAG_L001_R1_001.fastq -r HC_59_TAGTCTCC-TCATCGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_59
join_paired_ends.py -f HC_60_CGAGCGAC-GACACCGT_L001_R1_001.fastq -r HC_60_CGAGCGAC-GACACCGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_60
join_paired_ends.py -f HC_61_TAGTCTCC-CTGCGTGT_L001_R1_001.fastq -r HC_61_TAGTCTCC-CTGCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_61
join_paired_ends.py -f HC_62_TAGTCTCC-GGATATCT_L001_R1_001.fastq -r HC_62_TAGTCTCC-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_62
join_paired_ends.py -f HC_63_TAGTCTCC-TAGCGAGT_L001_R1_001.fastq -r HC_63_TAGTCTCC-TAGCGAGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_63
join_paired_ends.py -f HC_64_TGAGTACG-CTGCGTGT_L001_R1_001.fastq -r HC_64_TGAGTACG-CTGCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_64
join_paired_ends.py -f HC_65_CTGCGTAG-CGTGAGTG_L001_R1_001.fastq -r HC_65_CTGCGTAG-CGTGAGTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_65
join_paired_ends.py -f HC_66_ACGCTACT-CTGCGTGT_L001_R1_001.fastq -r HC_66_ACGCTACT-CTGCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_66
join_paired_ends.py -f HC_67_TAGTCTCC-CGTGAGTG_L001_R1_001.fastq -r HC_67_TAGTCTCC-CGTGAGTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_67
join_paired_ends.py -f HC_68_ACTCACTG-GGATATCT_L001_R1_001.fastq -r HC_68_ACTCACTG-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_68
join_paired_ends.py -f HC_69_ACGCTACT-TAGCGAGT_L001_R1_001.fastq -r HC_69_ACGCTACT-TAGCGAGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_69
join_paired_ends.py -f HC_70_ACGCTACT-GGATATCT_L001_R1_001.fastq -r HC_70_ACGCTACT-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_70
join_paired_ends.py -f HC_71_TGAGTACG-TCATCGAG_L001_R1_001.fastq -r HC_71_TGAGTACG-TCATCGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_71
join_paired_ends.py -f HC_72_GACATAGT-CTGCGTGT_L001_R1_001.fastq -r HC_72_GACATAGT-CTGCGTGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_72
join_paired_ends.py -f HC_73_CTGCGTAG-TCATCGAG_L001_R1_001.fastq -r HC_73_CTGCGTAG-TCATCGAG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_73
join_paired_ends.py -f HC_74_TGAGTACG-GGATATCT_L001_R1_001.fastq -r HC_74_TGAGTACG-GGATATCT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_74
join_paired_ends.py -f HC_75_ACTACGAC-CGTGAGTG_L001_R1_001.fastq -r HC_75_ACTACGAC-CGTGAGTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_75
join_paired_ends.py -f HC_76_CGAGCGAC-TAGCGAGT_L001_R1_001.fastq -r HC_76_CGAGCGAC-TAGCGAGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_76
join_paired_ends.py -f HC_77_CGAGCGAC-ACTATCTG_L001_R1_001.fastq -r HC_77_CGAGCGAC-ACTATCTG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_77
join_paired_ends.py -f HC_78_ACTACGAC-ATCGTACG_L001_R1_001.fastq -r HC_78_ACTACGAC-ATCGTACG_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_78
join_paired_ends.py -f HC_79_ACTACGAC-TAGCGAGT_L001_R1_001.fastq -r HC_79_ACTACGAC-TAGCGAGT_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_79
join_paired_ends.py -f HuntCr80_S87_L001_R1_001.fastq -r HuntCr80_S87_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_80
join_paired_ends.py -f HuntCr81_S60_L001_R1_001.fastq -r HuntCr81_S60_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_81
join_paired_ends.py -f HuntCr82_S122_L001_R1_001.fastq -r HuntCr82_S122_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_82
join_paired_ends.py -f HuntCr83_S112_L001_R1_001.fastq -r HuntCr83_S112_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_83
join_paired_ends.py -f HuntCr84_S58_L001_R1_001.fastq -r HuntCr84_S58_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_84
join_paired_ends.py -f HuntCr85_S178_L001_R1_001.fastq -r HuntCr85_S178_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_85
join_paired_ends.py -f HuntCr86_S119_L001_R1_001.fastq -r HuntCr86_S119_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_86
join_paired_ends.py -f HuntCr87_S35_L001_R1_001.fastq -r HuntCr87_S35_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_87
join_paired_ends.py -f HuntCr88_S51_L001_R1_001.fastq -r HuntCr88_S51_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_88
join_paired_ends.py -f HuntCr89_S187_L001_R1_001.fastq -r HuntCr89_S187_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_89
join_paired_ends.py -f HuntCr90_S137_L001_R1_001.fastq -r HuntCr90_S137_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_90
join_paired_ends.py -f HuntCr91_S80_L001_R1_001.fastq -r HuntCr91_S80_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_91
join_paired_ends.py -f HuntCr92_S6_L001_R1_001.fastq -r HuntCr92_S6_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_92
join_paired_ends.py -f HuntCr93_S62_L001_R1_001.fastq -r HuntCr93_S62_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_93
join_paired_ends.py -f HuntCr94_S4_L001_R1_001.fastq -r HuntCr94_S4_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_94
join_paired_ends.py -f HuntCr95_S84_L001_R1_001.fastq -r HuntCr95_S84_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_95
join_paired_ends.py -f HuntCr96_S52_L001_R1_001.fastq -r HuntCr96_S52_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_96
join_paired_ends.py -f HuntCr97_S164_L001_R1_001.fastq -r HuntCr97_S164_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_97
join_paired_ends.py -f HuntCr98_S44_L001_R1_001.fastq -r HuntCr98_S44_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_98
join_paired_ends.py -f HuntCr99_S86_L001_R1_001.fastq -r HuntCr99_S86_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_99
join_paired_ends.py -f HuntCr100_S40_L001_R1_001.fastq -r HuntCr100_S40_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_100
join_paired_ends.py -f HuntCr101_S68_L001_R1_001.fastq -r HuntCr101_S68_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_101
join_paired_ends.py -f HuntCr102_S64_L001_R1_001.fastq -r HuntCr102_S64_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_102
join_paired_ends.py -f HuntCr103_S166_L001_R1_001.fastq -r HuntCr103_S166_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_103
join_paired_ends.py -f HuntCr104_S48_L001_R1_001.fastq -r HuntCr104_S48_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_104
join_paired_ends.py -f HuntCr105_S66_L001_R1_001.fastq -r HuntCr105_S66_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_105
join_paired_ends.py -f HuntCr106_S162_L001_R1_001.fastq -r HuntCr106_S162_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_106
join_paired_ends.py -f HuntCr107_S46_L001_R1_001.fastq -r HuntCr107_S46_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_107
join_paired_ends.py -f HuntCr108_S110_L001_R1_001.fastq -r HuntCr108_S110_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_108
join_paired_ends.py -f HuntCr109_S81_L001_R1_001.fastq -r HuntCr109_S81_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_109
join_paired_ends.py -f HuntCr110_S7_L001_R1_001.fastq -r HuntCr110_S7_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_110
join_paired_ends.py -f HuntCr111_S100_L001_R1_001.fastq -r HuntCr111_S100_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_111
join_paired_ends.py -f HuntCr112_S118_L001_R1_001.fastq -r HuntCr112_S118_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_112
join_paired_ends.py -f HuntCr113_S70_L001_R1_001.fastq -r HuntCr113_S70_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_113
join_paired_ends.py -f HuntCr115_S72_L001_R1_001.fastq -r HuntCr115_S72_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_115
join_paired_ends.py -f HuntCr116_S116_L001_R1_001.fastq -r HuntCr116_S116_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_116
join_paired_ends.py -f HuntCr117_S22_L001_R1_001.fastq -r HuntCr117_S22_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_117
join_paired_ends.py -f HuntCr118_S136_L001_R1_001.fastq -r HuntCr118_S136_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_118
join_paired_ends.py -f HuntCr119_S190_L001_R1_001.fastq -r HuntCr119_S190_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_119
join_paired_ends.py -f HuntCr120_S112_L001_R1_001.fastq -r HuntCr120_S112_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_120
join_paired_ends.py -f HuntCr121_S71_L001_R1_001.fastq -r HuntCr121_S71_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_121
join_paired_ends.py -f HuntCr122_S34_L001_R1_001.fastq -r HuntCr122_S34_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_122
join_paired_ends.py -f HuntCr123_S78_L001_R1_001.fastq -r HuntCr123_S78_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_123
join_paired_ends.py -f HuntCr124_S30_L001_R1_001.fastq -r HuntCr124_S30_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_124
join_paired_ends.py -f HuntCr125_S8_L001_R1_001.fastq -r HuntCr125_S8_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_125
join_paired_ends.py -f HuntCr126_S104_L001_R1_001.fastq -r HuntCr126_S104_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_126
join_paired_ends.py -f HuntCr127_S108_L001_R1_001.fastq -r HuntCr127_S108_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_127
join_paired_ends.py -f HuntCr128_S6_L001_R1_001.fastq -r HuntCr128_S6_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_128
join_paired_ends.py -f HuntCr129_S128_L001_R1_001.fastq -r HuntCr129_S128_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_129
join_paired_ends.py -f HuntCr130_S174_L001_R1_001.fastq -r HuntCr130_S174_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_130
join_paired_ends.py -f HuntCr131_S16_L001_R1_001.fastq -r HuntCr131_S16_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_131
join_paired_ends.py -f HuntCr132_S54_L001_R1_001.fastq -r HuntCr132_S54_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_132
join_paired_ends.py -f HuntCr133_S126_L001_R1_001.fastq -r HuntCr133_S126_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_133
join_paired_ends.py -f HuntCr134_S10_L001_R1_001.fastq -r HuntCr134_S10_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_134
join_paired_ends.py -f HuntCr135_S80_L001_R1_001.fastq -r HuntCr135_S80_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_135
join_paired_ends.py -f HuntCr136_S12_L001_R1_001.fastq -r HuntCr136_S12_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_136
join_paired_ends.py -f HuntCr137_S58_L001_R1_001.fastq -r HuntCr137_S58_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_137
join_paired_ends.py -f HuntCr138_S152_L001_R1_001.fastq -r HuntCr138_S152_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_138
join_paired_ends.py -f HuntCr139_S60_L001_R1_001.fastq -r HuntCr139_S60_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_139
join_paired_ends.py -f HuntCr140_S148_L001_R1_001.fastq -r HuntCr140_S148_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_140
join_paired_ends.py -f HuntCr141_S130_L001_R1_001.fastq -r HuntCr141_S130_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_141
join_paired_ends.py -f HuntCr142_S42_L001_R1_001.fastq -r HuntCr142_S42_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_142
join_paired_ends.py -f HuntCr143_S142_L001_R1_001.fastq -r HuntCr143_S142_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_143
join_paired_ends.py -f HuntCr144_S138_L001_R1_001.fastq -r HuntCr144_S138_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_144
join_paired_ends.py -f HuntCr145_S114_L001_R1_001.fastq -r HuntCr145_S114_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_145
join_paired_ends.py -f HuntCr146_S94_L001_R1_001.fastq -r HuntCr146_S94_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_146
join_paired_ends.py -f HuntCr147_S188_L001_R1_001.fastq -r HuntCr147_S188_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_147
join_paired_ends.py -f HuntCr148_S38_L001_R1_001.fastq -r HuntCr148_S38_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_148
join_paired_ends.py -f HuntCr149_S14_L001_R1_001.fastq -r HuntCr149_S14_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_149
join_paired_ends.py -f HuntCr150_S182_L001_R1_001.fastq -r HuntCr150_S182_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_150
join_paired_ends.py -f HuntCr151_S24_L001_R1_001.fastq -r HuntCr151_S24_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_151
join_paired_ends.py -f HuntCr152_S90_L001_R1_001.fastq -r HuntCr152_S90_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_152
join_paired_ends.py -f HuntCr153_S140_L001_R1_001.fastq -r HuntCr153_S140_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_153
join_paired_ends.py -f HuntCr154_S20_L001_R1_001.fastq -r HuntCr154_S20_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_154
join_paired_ends.py -f HuntCr155_S134_L001_R1_001.fastq -r HuntCr155_S134_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_155
join_paired_ends.py -f HuntCr156_S156_L001_R1_001.fastq -r HuntCr156_S156_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_156
join_paired_ends.py -f HuntCr157_S160_L001_R1_001.fastq -r HuntCr157_S160_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_157
join_paired_ends.py -f HuntCr158_S158_L001_R1_001.fastq -r HuntCr158_S158_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_158
join_paired_ends.py -f HuntCr159_S180_L001_R1_001.fastq -r HuntCr159_S180_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_159
join_paired_ends.py -f HuntCr160_S186_L001_R1_001.fastq -r HuntCr160_S186_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_160
join_paired_ends.py -f HuntCr161_S92_L001_R1_001.fastq -r HuntCr161_S92_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_161
join_paired_ends.py -f HuntCr162_S88_L001_R1_001.fastq -r HuntCr162_S88_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_162
join_paired_ends.py -f HuntCr163_S184_L001_R1_001.fastq -r HuntCr163_S184_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_163
join_paired_ends.py -f HuntCr164_S18_L001_R1_001.fastq -r HuntCr164_S18_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_164
join_paired_ends.py -f HuntCr165_S62_L001_R1_001.fastq -r HuntCr165_S62_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_165
join_paired_ends.py -f HuntCr166_S84_L001_R1_001.fastq -r HuntCr166_S84_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_166
join_paired_ends.py -f HuntCr167_S154_L001_R1_001.fastq -r HuntCr167_S154_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_167
join_paired_ends.py -f HuntCr168_S32_L001_R1_001.fastq -r HuntCr168_S32_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_168
join_paired_ends.py -f HuntCr169_S11_L001_R1_001.fastq -r HuntCr169_S11_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_169
join_paired_ends.py -f HuntCr170_S132_L001_R1_001.fastq -r HuntCr170_S132_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_170
join_paired_ends.py -f HuntCr171_S56_L001_R1_001.fastq -r HuntCr171_S56_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_171
join_paired_ends.py -f HuntCr172_S65_L001_R1_001.fastq -r HuntCr172_S65_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_172
join_paired_ends.py -f HuntCr173_S159_L001_R1_001.fastq -r HuntCr173_S159_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_173
join_paired_ends.py -f HuntCr174_S91_L001_R1_001.fastq -r HuntCr174_S91_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_174
join_paired_ends.py -f HuntCr175_S106_L001_R1_001.fastq -r HuntCr175_S106_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_175
join_paired_ends.py -f HuntCr176_S124_L001_R1_001.fastq -r HuntCr176_S124_L001_R2_001.fastq -m SeqPrep -o HC_fastq-join_joined/HC_176
################################
# 3. validate mapping file
cd ~/Desktop/
validate_mapping_file.py -m Hunt_Creek_Map_R1.txt -o check.tab_mapping
validate_mapping_file.py -m Hunt_Creek_Map_R2.txt -o check.tab_mapping
validate_mapping_file.py -m Hunt_Creek_Map_R3.txt -o check.tab_mapping
validate_mapping_file.py -m Hunt_Creek_Map_R4.txt -o check.tab_mapping
validate_mapping_file.py -m Hunt_Creek_Map_R5.txt -o check.tab_mapping
validate_mapping_file.py -m Hunt_Creek_Map_R6.txt -o check.tab_mapping
validate_mapping_file.py -m Hunt_Creek_Map_R7.txt -o check.tab_mapping
################################
# 4. Demultiplexing and quality filtering (at Phred >= Q20) - use the *.join.fastq file after re-naming the file and moving those files to the desktop folder named "Joined", then cd ~/Desktop/Joined
cd ~/Desktop/Joined/
# split_libraries_fastq.py -i HC.txt -o /map/ -m map_HC.txt
split_libraries_fastq.py -i HC_1.gz --sample_id HC.1 -o ~/Desktop/Demultiplexed/HC/HC_1_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_2.gz --sample_id HC.2 -o ~/Desktop/Demultiplexed/HC/HC_2_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_3.gz --sample_id HC.3 -o ~/Desktop/Demultiplexed/HC/HC_3_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_4.gz --sample_id HC.4 -o ~/Desktop/Demultiplexed/HC/HC_4_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_5.gz --sample_id HC.5 -o ~/Desktop/Demultiplexed/HC/HC_5_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_6.gz --sample_id HC.6 -o ~/Desktop/Demultiplexed/HC/HC_6_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_7.gz --sample_id HC.7 -o ~/Desktop/Demultiplexed/HC/HC_7_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_8.gz --sample_id HC.8 -o ~/Desktop/Demultiplexed/HC/HC_8_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_9.gz --sample_id HC.9 -o ~/Desktop/Demultiplexed/HC/HC_9_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_10.gz --sample_id HC.10 -o ~/Desktop/Demultiplexed/HC/HC_10_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_11.gz --sample_id HC.11 -o ~/Desktop/Demultiplexed/HC/HC_11_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_12.gz --sample_id HC.12 -o ~/Desktop/Demultiplexed/HC/HC_12_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R1.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_13.gz --sample_id HC.13 -o ~/Desktop/Demultiplexed/HC/HC_13_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_14.gz --sample_id HC.14 -o ~/Desktop/Demultiplexed/HC/HC_14_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_15.gz --sample_id HC.15 -o ~/Desktop/Demultiplexed/HC/HC_15_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_16.gz --sample_id HC.16 -o ~/Desktop/Demultiplexed/HC/HC_16_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_17.gz --sample_id HC.17 -o ~/Desktop/Demultiplexed/HC/HC_17_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_18.gz --sample_id HC.18 -o ~/Desktop/Demultiplexed/HC/HC_18_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_19.gz --sample_id HC.19 -o ~/Desktop/Demultiplexed/HC/HC_19_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_20.gz --sample_id HC.20 -o ~/Desktop/Demultiplexed/HC/HC_20_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_21.gz --sample_id HC.21 -o ~/Desktop/Demultiplexed/HC/HC_21_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R2.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_22.gz --sample_id HC.22 -o ~/Desktop/Demultiplexed/HC/HC_22_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_23.gz --sample_id HC.23 -o ~/Desktop/Demultiplexed/HC/HC_23_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_24.gz --sample_id HC.24 -o ~/Desktop/Demultiplexed/HC/HC_24_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_25.gz --sample_id HC.25 -o ~/Desktop/Demultiplexed/HC/HC_25_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_26.gz --sample_id HC.26 -o ~/Desktop/Demultiplexed/HC/HC_26_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_27.gz --sample_id HC.27 -o ~/Desktop/Demultiplexed/HC/HC_27_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_28.gz --sample_id HC.28 -o ~/Desktop/Demultiplexed/HC/HC_28_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_29.gz --sample_id HC.29 -o ~/Desktop/Demultiplexed/HC/HC_29_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_30.gz --sample_id HC.30 -o ~/Desktop/Demultiplexed/HC/HC_30_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_31.gz --sample_id HC.31 -o ~/Desktop/Demultiplexed/HC/HC_31_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_32.gz --sample_id HC.32 -o ~/Desktop/Demultiplexed/HC/HC_32_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_33.gz --sample_id HC.33 -o ~/Desktop/Demultiplexed/HC/HC_33_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_34.gz --sample_id HC.34 -o ~/Desktop/Demultiplexed/HC/HC_34_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_35.gz --sample_id HC.35 -o ~/Desktop/Demultiplexed/HC/HC_35_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_36.gz --sample_id HC.36 -o ~/Desktop/Demultiplexed/HC/HC_36_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_37.gz --sample_id HC.37 -o ~/Desktop/Demultiplexed/HC/HC_37_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_38.gz --sample_id HC.38 -o ~/Desktop/Demultiplexed/HC/HC_38_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_39.gz --sample_id HC.39 -o ~/Desktop/Demultiplexed/HC/HC_39_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_40.gz --sample_id HC.40 -o ~/Desktop/Demultiplexed/HC/HC_40_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_41.gz --sample_id HC.41 -o ~/Desktop/Demultiplexed/HC/HC_41_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_42.gz --sample_id HC.42 -o ~/Desktop/Demultiplexed/HC/HC_42_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_43.gz --sample_id HC.43 -o ~/Desktop/Demultiplexed/HC/HC_43_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_44.gz --sample_id HC.44 -o ~/Desktop/Demultiplexed/HC/HC_44_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_45.gz --sample_id HC.45 -o ~/Desktop/Demultiplexed/HC/HC_45_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_46.gz --sample_id HC.46 -o ~/Desktop/Demultiplexed/HC/HC_46_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_47.gz --sample_id HC.47 -o ~/Desktop/Demultiplexed/HC/HC_47_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_48.gz --sample_id HC.48 -o ~/Desktop/Demultiplexed/HC/HC_48_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_49.gz --sample_id HC.49 -o ~/Desktop/Demultiplexed/HC/HC_49_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_50.gz --sample_id HC.50 -o ~/Desktop/Demultiplexed/HC/HC_50_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'
split_libraries_fastq.py -i HC_51.gz --sample_id HC.51 -o ~/Desktop/Demultiplexed/HC/HC_51_q20 -m ~/Desktop/Joined/Hunt_Creek_Map_R3.txt -q 19 --barcode_type 'not-barcoded'