Script to assemble processed transcriptome files via a loop in Trinit…

…y v2.8.4

BashScript_Loop_Trinity.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+TRINITYFOLDER=~/Programme/trinityrnaseq-Trinity-v2.8.4/ 
+ASSEMBLY_BASE=03_Assemblies
+
+if [ ! -e ${ASSEMBLY_BASE} ]
+then
+	mkdir ${ASSEMBLY_BASE}
+fi
+
+for R1 in 01_Data_Processed/*1P*
+do
+	R2=${R1//1P.fastq.gz/2P.fastq.gz}
+	OUTDIR=${ASSEMBLY_BASE}/${R1//1P.fastq.gz/Trinity}
+
+	echo ${TRINITY_FOLDER}/Trinity --seqType fq --max_memory 120G --min_contig_length 200 --CPU 56 --left 01_Data_Processed/$R1 --right 01_Data_Processed/$R2 --output ${OUTDIR} 
+
+
+
+done
+
+
+# Loop script to automatically run Trinity in a loop for fastq1_fw and fastq2_rv files.
+# The folder of the local Trinity installation is used to start Trinity (TRINITYFOLDER)
+# Processed and trimmed fastq files (*.fastq.gz) are located in the folder 01_Data_Processed/
+# Trinity settings are for phylogenomic analyses (transcripts len >200 bp) 
+# V.01 - 11.02.2019 - BMvR