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useq_bisulfite_cmd.txt
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#c kingspeak_24
# VERSION 2 TP
### Sample information
# substitute as appropriate
NAME=MYNAME
### Applications
JAVA=/usr/bin/java
APP=/tomato/dev/app
PICARD=/tomato/dev/app/picard/2.18.26/picard.jar
USEQ=$APP/useq/9.1.3/Apps
### Mouse mm10 data
DATA=/tomato/dev/data
INDEX=$DATA/Mouse/Mm10/mm10NormChrLambdaPhiXAdapt.nov.bisulphite.nix
VERSION='M_musculus_Dec_2010'
# special UCSC fasta folder with individual chromosome fastas plus lambda
FASTA=/uufs/chpc.utah.edu/common/home/hcibcore/Genomes/Mouse/mm10
### Human hg19 data
# DATA=/tomato/dev/data
# INDEX=$DATA/Human/Hg19/hg19NormChrLambPhiAdapt.nov.bisulphite.nix
# VERSION='H_sapiens_Feb_2009'
# # special UCSC fasta folder with individual chromosome fastas plus lambda
# FASTA=/uufs/chpc.utah.edu/common/home/hcibcore/Genomes/H_sapiens/Hg19/Fasta
### Zebrafish Zv10 data
# DATA=/tomato/dev/data
# INDEX=$DATA/Zebrafish/Zv10/zv10StdChrLambPhiAdapt.nov.bisulphite.nix
# VERSION='D_rerio_Sep_2014'
# # special UCSC fasta folder with individual chromosome fastas plus lambda
# FASTA=/uufs/chpc.utah.edu/common/home/hcibcore/Genomes/Zebrafish/Zv10/Fasta
# remove duplicates
echo; echo "======= Running Picard Mark Duplicates ======="
$JAVA -Xmx${SMGB}G \
-jar $PICARD MarkDuplicates \
I=$NAME.bam \
O=$NAME.dedup.bam \
M=${NAME}_dup_metrics.txt \
REMOVE_DUPLICATES=true ASSUME_SORTED=true
# Novoalign Bisulfite Parser
# increase base qualities to 20 and alignment score
echo; echo "====== Running USeq NovoalignBisulfiteParser ======"
$JAVA -Xmx${SMGB}G \
-jar $USEQ/NovoalignBisulfiteParser \
-a $NAME.dedup.bam \
-v $VERSION \
-f $FASTA \
-s ${NAME}_Parsed \
-b 20 -c 20 -x 360 -q 13 > ${NAME}_NovoalignBisulfiteParser.out.txt
# Parse CpG context
echo; echo "====== Running USeq ParsePointDataContexts for CpG ======"
$JAVA -Xmx${SMGB}G \
-jar $USEQ/ParsePointDataContexts \
-p ${NAME}_Parsed/ConvertedC \
-s ${NAME}_Parsed/ConvertedCpG \
-f $FASTA \
-c '..CG.'
$JAVA -Xmx${SMGB}G \
-jar $USEQ/ParsePointDataContexts \
-p ${NAME}_Parsed/NonConvertedC \
-s ${NAME}_Parsed/NonConvertedCpG \
-f $FASTA \
-c '..CG.'
# BisStat
echo; echo "====== Running USeq BisStat ======"
# BisStat on everything
$JAVA -Xmx${SMGB}G \
-jar $USEQ/BisStat \
-s ${NAME}_BisStatAll \
-c ${NAME}_Parsed/ConvertedC \
-n ${NAME}_Parsed/NonConvertedC \
-f $FASTA \
-l -o 4 > ${NAME}_BisStat.all.out.txt
# BisStat on CpG
$JAVA -Xmx${SMGB}G \
-jar $USEQ/BisStat \
-s ${NAME}_BisStatCpG \
-c ${NAME}_Parsed/ConvertedCpG \
-n ${NAME}_Parsed/NonConvertedCpG \
-f $FASTA \
-l -o 4 > ${NAME}_BisStat.CpG.out.txt
# Convert to USeq files
echo; echo "====== Running USeq convertors ======"
$JAVA -Xmx${SMGB}G \
-jar $USEQ/Bar2USeq \
-f ${NAME}_Parsed
# Convert to USeq files
echo; echo "====== Running BigWig convertors ======"
$JAVA -Xmx16G \
-jar $USEQ/USeq2UCSCBig \
-u ${NAME}_Parsed \
-d $APP/UCSC
$JAVA -Xmx16G \
-jar $USEQ/USeq2UCSCBig \
-u ${NAME}_BisStatAll \
-d $APP/UCSC
$JAVA -Xmx16G \
-jar $USEQ/USeq2UCSCBig \
-u ${NAME}_BisStatCpG \
-d $APP/UCSC