WIP: added general files descriptions #7
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#!/usr/bin/perl -w
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use strict;
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# this script was made with consideration for UMI-deduplicating.
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# this is because there are three .fastq files for each sample.
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# the provider states the info about which file contains which info,
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# but in our case, from GenomeScan in Leiden, R2 contains the UMI read.
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# R1 and R3 contain sequencing information from paired-end sequencing
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foreach my $file1 ( <*_R1.fastq.gz> ) {
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my $file2 = $file1;
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$file2 =~ s/\_R1\./_R2./;
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my $file3 =~ s/\_R3\./_R2./;
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die "file1==file2" if $file1 eq $file2;
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my $sample = $file1;
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$sample =~ s/\_R1\.fastq\.gz$//;
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H.C. Donker
commented
Is this case sensitive? Is this case sensitive?
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mkdir $sample.'_R1', 0700;
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system join(' ', 'fastqc', '-o', $sample.'_R1', $file1);
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mkdir $sample.'_R2', 0700;
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system join(' ', 'fastqc', '-o', $sample.'_R2', $file2);
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mkdir $sample.'_R3', 0700;
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system join(' ', 'fastqc', '-o', $sample.'_R3', $file3)
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}
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#!/bin/bash
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#SBATCH --job-name=FastQC.for.alveolar_type_2
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H.C. Donker
commented
Remove all the slurm comments. Remove all the slurm comments.
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#SBATCH --comment=FastQC.for.alveolar_type_2
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#SBATCH --time=48:00:00
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#SBATCH --mincpus=2
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#SBATCH --mem=20G
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#SBATCH --qos=priority
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# For 173 samples, it will take about 24 hrs to run with about 15Gb of memory.
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# Should probably parallelize the perl script/make it a bash/slurm script.
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module purge
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module load Perl/5.26.2-foss-2015b-bare
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module load BioPerl/1.6.924-foss-2015b-Perl-5.22.0
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H.C. Donker
commented
Do you really need BioPerl as well? Do you really need BioPerl as well?
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module load Java/11.0.2
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module load FastQC/0.11.7-Java-1.8.0_144-unlimited_JCE
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# Please see
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# https://www.youtube.com/watch?v=0Rj_xNuyOyQ
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cd /groups/umcg-griac/tmp04/projects/umcg-rbults/alveolar_type2_fastq/
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perl scripts/00_fastqc.pl
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mkdir rene_FastQC.results
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find . -maxdepth 1 -type d -iname "*_R[123]" -exec mv {} ./rene_FastQC.results/ \;
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H.C. Donker
commented
Remove anything that refers to your project dir/ you as a user in specific, and keep it general. Remove anything that refers to your project dir/ you as a user in specific, and keep it general.
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#find . -maxdepth 1 -type f -iname "*.htm*" -exec mv {} ./FastQC.results/ \;
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H.C. Donker
commented
Remove comments that are not necessary, or add comments what it can be used for. Remove comments that are not necessary, or add comments what it can be used for.
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