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

if (!$out) {

	die "USAGE: option --out is required.\n";

}

my @indices = @{ $index };

#checking option quality

if (-e $out && -d $out) {

print LOG "#####TrimSeq4scRNAseq.pl LOG#####\n";

print LOG "R1 file:\t$r1\n";

print LOG "R2 file:\t$r2\n";

print LOG "Index sequence:\t$index\n";

print LOG "Index sequence:\t@indices\n";

print LOG "\n";

print LOG "Tool versions:\n";

print LOG "\tFASTQC $fastqc_version\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;