for custom fastq/BAM File

#!/usr/bin/perl

# LMU Munich. AG Enard

# A script to filter reads based on Barcode base quality.

# Author: Swati Parekh

# Contact: parekh@bio.lmu.de or ziegenhain@bio.lmu.de or hellmann@bio.lmu.de

if(@ARGV != 4)

{

print 

"\n#####################################################################################

Usage: perl $0 <barcode-Read.fq.gz> <cDNA-Read.fq.gz> <StudyName> <Outdir> \n

Explanation of parameter:

barcode-Read.fq.gz	- Input barcode reads fastq file name.

cDNA-Read.fq.gz		- Input cDNA reads fastq file name.

Study       - Study name.

OUTDIR      - Output directory.

Please drop your suggestions and clarifications to <parekh\@bio.lmu.de>\n

######################################################################################\n\n";

exit;

}

$bcread=$ARGV[0];

$cdnaread=$ARGV[1];

$study=$ARGV[2];

$outdir=$ARGV[3];

$bcreadout = $outdir."/".$study.".barcodelist.filtered.sam";

if ($bcread =~ /\.gz$/) {

open BCF, '-|', 'gzip', '-dc', $bcread || die "Couldn't open file $bcread. Check permissions!\n Check if it is differently zipped then .gz\n\n";

open CDF, '-|', 'gzip', '-dc', $cdnaread || die "Couldn't open file $cdnaread. Check permissions!\n Check if it is differently zipped then .gz\n\n";

}

else {

open BCF, "<", $bcread || die "Couldn't open file $bcread. Check permissions!\n Check if it is differently zipped then .gz\n\n";

open CDF, "<", $cdnaread || die "Couldn't open file $cdnaread. Check permissions!\n Check if it is differently zipped then .gz\n\n";

}

open BCOUT, ">", $bcreadout || die "Couldn't open file $bcreadout to write\n\n";;

while(<BCF>){

	$brid=$_;

	$brseq=<BCF>;

	$bqid=<BCF>;

	$bqseq=<BCF>;

	$crid=<CDF>;

	$crseq=<CDF>;

	$cqid=<CDF>;

	$cqseq=<CDF>;

	@c = split(/\/|\s/,$crid);

	@b = split(/\/|\s/,$brid);

	if($c[0] eq $b[0]){ 

		$brid =~ m/^@(.*)\s/; chomp($brseq);

		print BCOUT $1,"\t4\t*\t0\t0\t*\t*\t0\t0\t$brseq\t$bqseq";

	}

	else

	{

		print "ERROR! Fastq files are not in the same order.\n Make sure to provide reads in the same order.\n\n";

		last;

	}

}

close BCF;

close CDF;

close BCOUT;

#!/bin/bash

f1=$1

f2=$2

sn=$3

o=$4

d=$5

# MAKING THE HEADER

echo '#!/bin/bash' >$o/$sn.prep.sh

echo '#SBATCH -n 1' >>$o/$sn.prep.sh

echo '#SBATCH --error='prep'.%J.err' >>$o/$sn.prep.sh

echo '#SBATCH --output='prep'.%J.out' >>$o/$sn.prep.sh

echo '#SBATCH --workdir='$o >>$o/$sn.prep.sh

echo "srun perl $d/fqcheck.pl $f1 $f2 $sn $o" >>$o/$sn.prep.sh

sbatch $o/$sn.prep.sh > $o/$sn.preparejobid.txt