added extra sequences to trim for TrimSeq4scRNAseq.pl

my $polyA = "AAAAAAAAAAAAAAA";

my $polyT = "TTTTTTTTTTTTTTT";

my $univ_adapter = "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT";

my $univ_adapter_rc = reverse $univ_adapter;

$univ_adapter_rc =~ tr/ATGC/TACG/;

my $se_pcr_primer1 = "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT";

my $se_pcr_primer1_rc = reverse $se_pcr_primer1;

$se_pcr_primer1_rc =~ tr/ATGC/TACG/;

my $rna_pcr_primer = "AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA";

my $rna_pcr_primer_rc = reverse $rna_pcr_primer;

$rna_pcr_primer_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/;

my $nextera_transposase_2_rc = reverse $nextera_transposase_2;

$nextera_transposase_2_rc =~ tr/ATGC/TACG/;

my $univ_adapter = "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT";

my $univ_adapter_rc = reverse $univ_adapter;

$univ_adapter_rc =~ tr/ATGC/TACG/;

my $clontech_univ_primer_long = "CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGT";

my $clontech_univ_primer_long_rc = reverse $clontech_univ_primer_long;

$clontech_univ_primer_long_rc =~ tr/ATGC/TACG/;

my $smart_cds_primer_ii_a = "AAGCAGTGGTATCAACGCAGAGTACT";

my $smart_cds_primer_ii_a_rc = reverse $smart_cds_primer_ii_a;

$smart_cds_primer_ii_a_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/;

print TRIMMINGS "$polyA\n";

print TRIMMINGS ">Ts\n";

print TRIMMINGS "$polyT\n";

print TRIMMINGS ">IlluminaUniversalAdapter\n";

print TRIMMINGS "$univ_adapter\n";

print TRIMMINGS ">IlluminaUniversalAdapter_rc\n";

print TRIMMINGS "$univ_adapter_rc\n";

print TRIMMINGS ">IlluminaSEPCRPrimer1\n";

print TRIMMINGS "$se_pcr_primer1\n";

print TRIMMINGS ">IlluminaSEPCRPrimer1_rc\n";

print TRIMMINGS "$se_pcr_primer1_rc\n";

print TRIMMINGS ">IlluminaRNAPCRPrimer\n";

print TRIMMINGS "$rna_pcr_primer\n";

print TRIMMINGS ">IlluminaRNAPCRPrimer_rc\n";

print TRIMMINGS "$rna_pcr_primer_rc\n";

print TRIMMINGS ">NexteraTransposaseRead1\n";

print TRIMMINGS "$nextera_transposase_1\n";

print TRIMMINGS ">NexteraTransposaseRead1_rc\n";

print TRIMMINGS "$nextera_transposase_2\n";

print TRIMMINGS ">NexteraTransposaseRead2_rc\n";

print TRIMMINGS "$nextera_transposase_2_rc\n";

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";

	my $nextera_pcr_primer_i7_rc = reverse $nextera_pcr_primer_i7;

	print TRIMMINGS ">NexTera_PCR_primer_i7_rc_$ind\n";

	print TRIMMINGS "$nextera_pcr_primer_i7_rc\n";

}

print TRIMMINGS ">ClontechUniversalPrimerLong\n";

print TRIMMINGS "$clontech_univ_primer_long\n";

print TRIMMINGS ">ClontechUniversalPrimerLong_rc\n";

print TRIMMINGS "$clontech_univ_primer_long_rc\n";

print TRIMMINGS ">SMART_CDS_primer_IIA\n";

print TRIMMINGS "$smart_cds_primer_ii_a\n";

print TRIMMINGS ">SMART_CDS_primer_IIA_rc\n";

print TRIMMINGS "$smart_cds_primer_ii_a_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";

close (TRIMMINGS);

#run scythe