Merge branch 'master' of github.com:kbattenb/universc (b3035cd3) · Commits · github_fork / Universc

sub/TrimSeq4scRNAseq.pl

+8 −0

Original line number	Diff line number	Diff line
		@@ -180,6 +180,10 @@ my $univ_adapter = "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT";
		my $univ_adapter_rc = reverse $univ_adapter;
		$univ_adapter_rc =~ tr/ATGC/TACG/;

		my $smarter_ii_a_oligo = "AAGCAGTGGTATCAACGCAGAGTAC";
		my $smarter_ii_a_oligo_rc = reverse $smarter_ii_a_oligo;
		$smarter_ii_a_oligo_rc =~ tr/ATGC/TACG/;

		open (TRIMMINGS, ">", "$trimmings") or die "cannot open $trimmings\n";
		print TRIMMINGS ">As\n";
		print TRIMMINGS "$polyA\n";
		@@ -197,6 +201,10 @@ print TRIMMINGS ">IlluminaUniversalAdapter\n";
		print TRIMMINGS "$univ_adapter\n";
		print TRIMMINGS ">IlluminaUniversalAdapter_rc\n";
		print TRIMMINGS "$univ_adapter_rc\n";
		print TRIMMINGS ">SMARTer_II_A_oligo\n";
		print TRIMMINGS "$smarter_ii_a_oligo\n";
		print TRIMMINGS ">SMARTer_II_A_oligo_rc\n";
		print TRIMMINGS "$smarter_ii_a_oligo_rc\n";

		foreach my $ind (@indices) {
		my $nextera_pcr_primer_i7 = "CAAGCAGAAGACGGCATACGAGAT".$ind."GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG";