added fastQC code snippet (.pl and .sh scripts)
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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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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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#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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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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#find . -maxdepth 1 -type f -iname "*.htm*" -exec mv {} ./FastQC.results/ \;
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