Mercurial > repos > brasset_jensen > srnapipe

comparison bin/sRNAPipe.pl @ 36:82779d2aacdd draft

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Uploaded
author brasset_jensen
date Sun, 17 Jun 2018 16:39:58 -0400
parents 54cb93674556
children 4bc00caa60b4
comparison
equal deleted inserted replaced
35:360ec0ae04c9 36:82779d2aacdd
203 extract_sam ( $type_sequence_hashP, $sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); 203 extract_sam ( $type_sequence_hashP, $sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq );
204 extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); 204 extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq );
205 } 205 }
206 206
207 my $ex_count_file = $type_dir.$type_prefix.'transcripts_reads_counts.txt'; 207 my $ex_count_file = $type_dir.$type_prefix.'transcripts_reads_counts.txt';
208 my ( $ex_count, $ex_ref_size ) = sam_count ( $type_sam_transcripts ); 208 my ( $ex_count, $ex_ref_size ) = sam_count_mis ( $type_sam_transcripts );
209 rpms_rpkm_te( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo ); 209 rpms_rpkm_te( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo );
210 210
211 my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs ); 211 my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs );
212 my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt'; 212 my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt';
213 my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt'; 213 my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt';