From 51abdcdb26e9da5b7d74b0f2626e56d3cbfa254d Mon Sep 17 00:00:00 2001
From: Jos van Nijnatten <spam@euphemism-inc.nl>
Date: Mon, 15 Feb 2021 16:48:39 +0100
Subject: [PATCH 1/2] Trimmomatic update (simplified)

---
 rnaseq/step2_trim/snippet.sh | 60 ++++++++++++++++++------------------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/rnaseq/step2_trim/snippet.sh b/rnaseq/step2_trim/snippet.sh
index 810c087..ebf0200 100644
--- a/rnaseq/step2_trim/snippet.sh
+++ b/rnaseq/step2_trim/snippet.sh
@@ -1,36 +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
+# reference: http://www.usadellab.org/cms/?page=trimmomatic
 
-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
+module load Trimmomatic
 
-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
+# (Example) Paired end
+java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
+  -phred33 \
+  input_forward.fq.gz \
+  input_reverse.fq.gz \
+  output_forward_paired.fq.gz \
+  output_forward_unpaired.fq.gz \
+  output_reverse_paired.fq.gz \
+  output_reverse_unpaired.fq.gz \
+  ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 \
+  LEADING:3 \
+  TRAILING:3 \
+  SLIDINGWINDOW:4:25 \
+  HEADCROP:8 \
+  MINLEN:50
+
+
+# (Example) Single end
+java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar SE \
+  -phred33 \
+  input.fq.gz \
+  output.fq.gz \
+  ILLUMINACLIP:TruSeq3-SE:2:30:10 \
+  LEADING:3 \
+  TRAILING:3 \
+  SLIDINGWINDOW:4:15 \
+  HEADCROP:8 \
+  MINLEN:50
-- 
2.40.1


From 6cf40804c47c573c965aadbff3f4b4e55d6285ba Mon Sep 17 00:00:00 2001
From: Jos van Nijnatten <spam@euphemism-inc.nl>
Date: Mon, 15 Feb 2021 17:03:34 +0100
Subject: [PATCH 2/2] adapter comments

---
 rnaseq/step2_trim/snippet.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/rnaseq/step2_trim/snippet.sh b/rnaseq/step2_trim/snippet.sh
index ebf0200..1ae866f 100644
--- a/rnaseq/step2_trim/snippet.sh
+++ b/rnaseq/step2_trim/snippet.sh
@@ -6,6 +6,11 @@
 module load Trimmomatic
 
 
+# Adapters can be found at
+# https://github.com/timflutre/trimmomatic/tree/master/adapters
+# But should be verified with FastQC, or in another way.
+
+
 # (Example) Paired end
 java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
   -phred33 \
-- 
2.40.1