RNA-seq/03_mapping_script at main · mathilde733/RNA-seq · GitHub

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#!/bin/bash

#SBATCH --mail-type=none
#SBATCH --job-name="mapping"
#SBATCH --nodes=1
#SBATCH --cpus-per-task=12
#SBATCH --time=12:00:00
#SBATCH --mem=64G
#SBATCH --ntasks=1
#SBATCH --partition=pibu_el8

#IMPORTANT: you have to download the reference genome and the annotation file from ENSEMBL before running this script (details are on README.md)
apptainer exec --bind /data/ /containers/apptainer/hisat2_samtools_408dfd02f175cd88.sif hisat2-build ./Mus_musculus.GRCm39.dna.primary_assembly.fa ./reference_index

for id in SRR7821918 SRR7821919 SRR7821920 SRR7821921 SRR7821922 SRR7821937 SRR7821938 SRR7821939 SRR7821949 SRR7821950 SRR7821951 SRR7821952 SRR7821953 SRR7821968 SRR7821969 SRR7821970
do
  apptainer exec --bind /data/ /containers/apptainer/hisat2_samtools_408dfd02f175cd88.sif hisat2 -x /data/users/mjacquey/RNA_seq_project/mapping/reference_index -1 \
/data/users/mjacquey/RNA_seq_project/trim_result/${id}_1trim.fastq.gz -2 /data/users/mjacquey/RNA_seq_project/trim_result/${id}_2trim.fastq.gz \
-S /data/users/mjacquey/RNA_seq_project/mapping/result/${id}_aligned_reads.sam -p 12 --rna-strandness RF
  apptainer exec --bind /data/ /containers/apptainer/hisat2_samtools_408dfd02f175cd88.sif samtools view \
-hbS /data/users/mjacquey/RNA_seq_project/mapping/result/${id}*.sam > /data/users/mjacquey/RNA_seq_project/mapping/result/${id}.bam
  apptainer exec --bind /data/ /containers/apptainer/hisat2_samtools_408dfd02f175cd88.sif samtools sort -m 32G -@ 12 \
-o /data/users/mjacquey/RNA_seq_project/mapping/result/${id}sorted.bam -T temp /data/users/mjacquey/RNA_seq_project/mapping/result/${id}.bam
  apptainer exec --bind /data/ /containers/apptainer/hisat2_samtools_408dfd02f175cd88.sif samtools index /data/users/mjacquey/RNA_seq_project/mapping/result/${id}sorted.bam
done