command for making an interleave file

[morning latte]

Hello,

I have two separate files containing R1 and R2 reads from HiSeq. The number of each file is different from QC. I have found few commands generating one interleave file from R1 and R2 files. But I also want to generate another file only with orphans rather than discarding them. Please give me direction to that script. Thank you.

[Kennels]

The software Trimmomatic can generate the orphans for you in addition to QC filter and removing adapters, all in one go. If you want interleaved PE reads, then just take the Paired files output and implement what you have already done on these.

[BugSeq]

I would recommend using filtering programs that keep track of the paired end relationship and separates them into another file when the mate doesn't meet your filtering requirements. I have had good luck with Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic).

With the pared files in hand a simple script is all that is needed to interleave them. The one below used to come with velvet.

#!/usr/bin/perl

if (!@ARGV) {
	print "Usage: $0 forward_reads.fa reverse_reaads.fa outfile.fa\n";
	print "\tforward_reads.fa / reverse_reads.fa : paired reads to be merged\n";
	print "\toutfile.fa : outfile to be created\n";
	system.exit(0);	
}

$filenameA = $ARGV[0];
$filenameB = $ARGV[1];
$filenameOut = $ARGV[2];

die "Could not open $filenameA" unless (-e $filenameA);
die "Could not open $filenameB" unless (-e $filenameB);

open FILEA, "< $filenameA";
open FILEB, "< $filenameB";

open OUTFILE, "> $filenameOut";

my ($lineA, $lineB);

$lineA = <FILEA>;
$lineB = <FILEB>;

while(defined $lineA) {
	print OUTFILE $lineA;
	$lineA = <FILEA>;
	while (defined $lineA && $lineA !~ m/>/) { 
		print OUTFILE $lineA;
		$lineA = <FILEA>;
	}

	print OUTFILE $lineB;
	$lineB = <FILEB>;
	while (defined $lineB && $lineB !~ m/>/) { 
		print OUTFILE $lineB;
		$lineB = <FILEB>;
	}
}