WIP: added general files descriptions #7

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R. Bults wants to merge 2 commits from p287376/system_genetics:master into master
3 changed files with 50 additions and 0 deletions

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#!/usr/bin/perl -w
use strict;
# this script was made with consideration for UMI-deduplicating.
# this is because there are three .fastq files for each sample.
# the provider states the info about which file contains which info,
Review

What do you mean with provider?

What do you mean with provider?
# but in our case, from GenomeScan in Leiden, R2 contains the UMI read.
# R1 and R3 contain sequencing information from paired-end sequencing
foreach my $file1 ( <*_R1.fastq.gz> ) {
my $file2 = $file1;
$file2 =~ s/\_R1\./_R2./;
my $file3 =~ s/\_R3\./_R2./;
die "file1==file2" if $file1 eq $file2;
my $sample = $file1;
$sample =~ s/\_R1\.fastq\.gz$//;
Review

Is this case sensitive?

Is this case sensitive?
mkdir $sample.'_R1', 0700;
system join(' ', 'fastqc', '-o', $sample.'_R1', $file1);
mkdir $sample.'_R2', 0700;
system join(' ', 'fastqc', '-o', $sample.'_R2', $file2);
mkdir $sample.'_R3', 0700;
system join(' ', 'fastqc', '-o', $sample.'_R3', $file3)
}

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#!/bin/bash
#SBATCH --job-name=FastQC.for.alveolar_type_2
Review

Remove all the slurm comments.

Remove all the slurm comments.
#SBATCH --comment=FastQC.for.alveolar_type_2
#SBATCH --time=48:00:00
#SBATCH --mincpus=2
#SBATCH --mem=20G
#SBATCH --qos=priority
# For 173 samples, it will take about 24 hrs to run with about 15Gb of memory.
# Should probably parallelize the perl script/make it a bash/slurm script.
module purge
module load Perl/5.26.2-foss-2015b-bare
module load BioPerl/1.6.924-foss-2015b-Perl-5.22.0
Review

Do you really need BioPerl as well?

Do you really need BioPerl as well?
module load Java/11.0.2
module load FastQC/0.11.7-Java-1.8.0_144-unlimited_JCE
# Please see
# https://www.youtube.com/watch?v=0Rj_xNuyOyQ
cd /groups/umcg-griac/tmp04/projects/umcg-rbults/alveolar_type2_fastq/
perl scripts/00_fastqc.pl
mkdir rene_FastQC.results
find . -maxdepth 1 -type d -iname "*_R[123]" -exec mv {} ./rene_FastQC.results/ \;
Review

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.
#find . -maxdepth 1 -type f -iname "*.htm*" -exec mv {} ./FastQC.results/ \;
Review

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.