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FastQC, Trimming, Overall QC (initial) #1

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J.v.N. merged 6 commits from P300299/system_genetics:master into master 2021-02-15 16:20:22 +01:00
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rnaseq/step2_trim/snippet.sh
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## this script is to generate jobs of trimming for each samples on the cluster
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H.C. Donker commented 2021-02-09 14:57:35 +01:00
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Perhaps write some instructions how to use. E.g., you need samples.csv.

Perhaps write some instructions how to use. E.g., you need `samples.csv`.
## please run this script first and then submit the jobs for each samples
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H.C. Donker commented 2021-02-09 15:03:47 +01:00
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Maybe a general question, do we want to:

  • provide am entire script that processes an entire batch of samples, or
  • do we want to focus on the core of trimming (only trim_galore/Trimmomatic command with options), and remove all the for loops and if-else statements?
Maybe a general question, do we want to: - provide am entire script that processes an entire batch of samples, or - do we want to focus on the core of trimming (only `trim_galore`/`Trimmomatic` command with options), and remove all the for loops and if-else statements?
## 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
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H.C. Donker commented 2021-02-09 14:56:26 +01:00
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Does this depend on sequencing machine/library type? If so, specify.

Does this depend on sequencing machine/library type? If so, specify.
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