added fastQC code snippet (.pl and .sh scripts)

rnaseq/step1_fastqc/00_fastqc.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --job-name=FastQC.for.alveolar_type_2
+#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
+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/ \;
+#find . -maxdepth 1 -type f -iname "*.htm*" -exec mv {} ./FastQC.results/ \;
+