Merge branch 'master' of github.com:kbattenb/universc

GetOptions (

	'r1=s' => \$r1,

	'r2=s' => \$r2,

	'index=s' => \$index,

	'index=s@' => \$index,

	'out=s' => \$out,

	'mode=s' => \$mode,

	'q_threshold=s' => \$q_threshold,

my $polyA = "AAAAAAAAAAAAAAA";

my $polyT = "TTTTTTTTTTTTTTT";

my $nextera_pcr_primer_i7 = "CAAGCAGAAGACGGCATACGAGAT".$index."GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG";

my $nextera_pcr_primer_i7_rc = reverse $nextera_pcr_primer_i7;

$nextera_pcr_primer_i7_rc =~ tr/ATGC/TACG/;

my $nextera_transposase_1 = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG";

my $nextera_transposase_1_rc = reverse $nextera_transposase_1;

$nextera_transposase_1_rc =~ tr/ATGC/TACG/;

print TRIMMINGS "$polyA\n";

print TRIMMINGS ">Ts\n";

print TRIMMINGS "$polyT\n";

print TRIMMINGS ">NexTera_PCR_primer_i7\n";

print TRIMMINGS "$nextera_pcr_primer_i7\n";

print TRIMMINGS ">NexTera_PCR_primer_i7_rc\n";

print TRIMMINGS "$nextera_pcr_primer_i7_rc\n";

print TRIMMINGS ">NexteraTransposaseRead1\n";

print TRIMMINGS "$nextera_transposase_1\n";

print TRIMMINGS ">NexteraTransposaseRead1_rc\n";

print TRIMMINGS ">IlluminaUniversalAdapter_rc\n";

print TRIMMINGS "$univ_adapter_rc\n";

my @indices = @{ $index };

foreach my $ind (@indices) {

	my $nextera_pcr_primer_i7 = "CAAGCAGAAGACGGCATACGAGAT".$ind."GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG";

	my $nextera_pcr_primer_i7_rc = reverse $nextera_pcr_primer_i7;

	$nextera_pcr_primer_i7_rc =~ tr/ATGC/TACG/;

	print TRIMMINGS ">NexTera_PCR_primer_i7_$ind\n";

	print TRIMMINGS "$nextera_pcr_primer_i7\n";

	print TRIMMINGS ">NexTera_PCR_primer_i7_rc_$ind\n";

	print TRIMMINGS "$nextera_pcr_primer_i7_rc\n";

}

close (TRIMMINGS);

#run scythe

print " running adapter trimming with scythe\n";

system "scythe -a $trimmings -q sanger -p $p_threshold -n $m_threshold -M $l_threshold --quiet $r2_raw_file | gzip >$r2_at_file";