@@ -0,0 +3,4 @@
+
+# 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,

@@ -0,0 +13,4 @@
+    my $file3 =~ s/\_R3\./_R2./;
+    die "file1==file2" if $file1 eq $file2;
+    my $sample = $file1;
+    $sample =~ s/\_R1\.fastq\.gz$//;

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --job-name=FastQC.for.alveolar_type_2

@@ -0,0 +11,4 @@
+
+module purge
+module load Perl/5.26.2-foss-2015b-bare
+module load BioPerl/1.6.924-foss-2015b-Perl-5.22.0

@@ -0,0 +22,4 @@
+perl scripts/00_fastqc.pl
+
+mkdir rene_FastQC.results
+find . -maxdepth 1 -type d -iname "*_R[123]" -exec mv {} ./rene_FastQC.results/ \;

@@ -0,0 +23,4 @@
+
+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/ \;