24 lines
884 B
Perl
Executable File
24 lines
884 B
Perl
Executable File
#!/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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