36 lines
1.5 KiB
Bash
36 lines
1.5 KiB
Bash
## this script is to generate jobs of trimming for each samples on the cluster
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## please run this script first and then submit the jobs for each samples
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## reference: http://www.usadellab.org/cms/?page=trimmomatic
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#!/bin/bash
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# $1 indicates the path of raw samples.
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# In the input folder, one sample has one independent folder with two pair-end f
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astq files.
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# The folder name should be the sample name.
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# the fastq file should be sample_1.fastq and sample_2.fastq
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# please prepare a sample.list that include file names for each sample
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out="/ * your output folder * /"
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input="/ * your input folder * /"
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cat sample.list | while read line
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do
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sample=$(echo $line)
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echo '#!/bin/bash' > rnaseq.${sample}.sh
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echo "#SBATCH --job-name=RNAseq.${sample}" >> rnaseq.${sample}.sh
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echo "#SBATCH --error=RNAseq.${sample}.err" >> rnaseq.${sample}.sh
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echo "#SBATCH --output=RNAseq.${sample}.out" >> rnaseq.${sample}.sh
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echo "#SBATCH --mem=15gb" >> rnaseq.${sample}.sh
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echo "#SBATCH --time=6:00:00" >> rnaseq.${sample}.sh
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echo "#SBATCH --cpus-per-task=6" >> rnaseq.${sample}.sh
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echo "ml Java" >>rnaseq.${sample}.sh
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echo "java -jar /* your folder of software */trimmomatic-0.36.jar PE \
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-phred33 /$input/${sample}\_1.fq.gz /$input/${sample}\_2.fq.gz \
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$out/trimmomatic/${sample}\_1_paired.fq $out/trimmomatic/${sample}\_1_unpaired.fq \
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$out/trimmomatic/${sample}\_2_paired.fq $out/trimmomatic/${sample}\_2_unpaired.fq \
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ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 \
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LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 HEADCROP:8 MINLEN:50" >> rnaseq.${sample}.sh
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done |