Mercurial > repos > brasset_jensen > srnapipe

comparison bin/sRNAPipe.pl @ 21:b80aa719069f draft

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Uploaded
author brasset_jensen
date Sun, 13 May 2018 15:40:38 -0400
parents 1df6aaac800e
children 6669c4f79cac
comparison
equal deleted inserted replaced
20:8ea13dab3435 21:b80aa719069f
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';
215 rpms_rpkm( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo ); 215 rpms_rpkm_te( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo );
216 rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo ); 216 rpms_rpkm_te( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo );
217 rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo ); 217 rpms_rpkm_te( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo );
218 218
219 sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child ); 219 sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child );
220 sam_sorted_bam ( $type_sam_transcripts, $grand_child ); sam_sorted_bam ( $type_sam_uni_transcripts, $grand_child ); 220 sam_sorted_bam ( $type_sam_transcripts, $grand_child ); sam_sorted_bam ( $type_sam_uni_transcripts, $grand_child );
221 sam_sorted_bam ( $type_sam_uni_TEs, $grand_child ); 221 sam_sorted_bam ( $type_sam_uni_TEs, $grand_child );
222 222