p287376/system_genetics
1
0
Fork 0
forked from GRIAC/system_genetics
Code Issues Pull Requests Projects Releases Wiki Activity

fastqc: simple comment. trimming: reverted back. overall qc: simplified the scripts and made sure to add instructions.

Browse Source
This commit is contained in:
Jos van Nijnatten
2021-02-10 13:42:51 +01:00
parent 135f231c86
commit 648cd09a0e
6 changed files with 64 additions and 813 deletions
Download Patch File Download Diff File Expand all files Collapse all files

37
rnaseq/step1_fastqc/snippet.sh
View File

@ -1,34 +1,5 @@
#!/bin/bash
#SBATCH --job-name=fastqc
#SBATCH --time=0-12:00:00
#SBATCH --ntasks=1
#SBATCH --mem=15G
#SBATCH --qos=regular
# The command to do a FastQC on a fastq file is
file="file_to_analyse.fq.gz"
fastqc_out="./path/to/fastqc/output/dir"
set -e
set -u
set -x
set -o pipefail
module purge
module load Java
module load FastQC
dir_raw_fastq="$(pwd)/fastq/raw"
dir_fastqc="$(pwd)/fastqc"
[ -d "${dir_fastqc}" ] || mkdir -p "${dir_fastqc}"
# Run FastQC
files=$(find -L "$dir_raw_fastq" -type f -iname "*.fastq.gz")
for file in $files; do
filename=$(basename "$file")
fastqc -o "$dir_fastqc" "$file" &
done
wait
fastqc -o "$fastqc_out" "$file"