Mercurial > repos > brasset_jensen > srnapipe
comparison bin/sRNAPipe.pl @ 34:54cb93674556 draft
Uploaded
author | brasset_jensen |
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date | Sun, 17 Jun 2018 16:32:54 -0400 |
parents | 6669c4f79cac |
children | 82779d2aacdd |
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33:c1a5c5205b24 | 34:54cb93674556 |
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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 ( $type_sam_transcripts ); |
209 rpms_rpkm( $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'; |
214 my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt'; | 214 my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt'; |