From 4b61c099f632956a6a063e9bf57e3e98fa49109c Mon Sep 17 00:00:00 2001
From: "C. Qi" <c.qi@rug.nl>
Date: Sat, 13 Feb 2021 19:13:13 +0100
Subject: [PATCH] Update 'rnaseq/step2_trim/snippet.sh'

---
 rnaseq/step2_trim/snippet.sh | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/rnaseq/step2_trim/snippet.sh b/rnaseq/step2_trim/snippet.sh
index e69de29..810c087 100644
--- a/rnaseq/step2_trim/snippet.sh
+++ b/rnaseq/step2_trim/snippet.sh
@@ -0,0 +1,36 @@
+## this script is to generate jobs of trimming for each samples on the cluster
+## please run this script first and then submit the jobs for each samples
+## reference: http://www.usadellab.org/cms/?page=trimmomatic
+
+#!/bin/bash
+# $1 indicates the path of raw samples. 
+# In the input folder, one sample has one independent folder with two pair-end f
+astq files. 
+# The folder name should be the sample name. 
+# the fastq file should be sample_1.fastq and sample_2.fastq 
+# please prepare a sample.list that include file names for each sample
+
+out="/ * your output folder * /"
+input="/ * your input folder * /"
+cat sample.list | while read line
+
+do
+sample=$(echo $line)
+echo '#!/bin/bash'  > rnaseq.${sample}.sh
+echo "#SBATCH --job-name=RNAseq.${sample}" >> rnaseq.${sample}.sh
+echo "#SBATCH --error=RNAseq.${sample}.err" >> rnaseq.${sample}.sh
+echo "#SBATCH --output=RNAseq.${sample}.out" >> rnaseq.${sample}.sh
+echo "#SBATCH --mem=15gb" >> rnaseq.${sample}.sh
+echo "#SBATCH --time=6:00:00" >> rnaseq.${sample}.sh
+echo "#SBATCH --cpus-per-task=6" >> rnaseq.${sample}.sh
+
+echo "ml Java" >>rnaseq.${sample}.sh
+
+echo "java -jar /* your folder of software */trimmomatic-0.36.jar PE \
+  -phred33 /$input/${sample}\_1.fq.gz /$input/${sample}\_2.fq.gz \
+   $out/trimmomatic/${sample}\_1_paired.fq $out/trimmomatic/${sample}\_1_unpaired.fq \
+   $out/trimmomatic/${sample}\_2_paired.fq $out/trimmomatic/${sample}\_2_unpaired.fq \
+   ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 \
+   LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 HEADCROP:8 MINLEN:50" >> rnaseq.${sample}.sh
+
+done
\ No newline at end of file