Man pages for khembach/DISCERNS
DISCovery of unannotated Exons from RNa-seq Splice junction reads
| create_tr_entry | Create a new GTF entry for a novel terminal exon |
| DISCERNS | DISCERNS |
| downstream_count | Count mapped parts in a read from max-1 to 0 in the most... |
| extend_gtf | Extend GTF file with predicted exons |
| filter_junction_reads | Junction reads from BAM file |
| filter_terminal_sj | Filter novel exon predictions of potential terminal exon |
| filter_trans_splice_junctions | Filter novel splice junctions based on overlapping genes |
| find_novel_exons | Novel exon prediction |
| get_reads | Import splice junction reads in a given genomic region |
| get_second_sj | Identify the second splice junction of a novel exon |
| identify_exon_end | Determine the coordinates of a novel exon at the end of a... |
| identify_exon_from_sj | Identify a novel exon from a single novel splice junction |
| identify_exon_start | Determine the coordinates of a novel exon at the start of a... |
| import_novel_sj_reads | Import reads with novel splice junctions |
| import_novel_sj_reads_parallel | Import reads with novel splice junctions in parallel |
| match_sj_in_intron | Match novel splice junctions within an intron |
| new_internal_transcript | Create new GTF annotation for a novel internal exon |
| new_left_terminal_transcript | Create new GTF annotation for a novel left terminal exon |
| new_right_terminal_transcript | Create new GTF annotation for a novel right terminal exon |
| predict_cassette_exon | Predict novel cassette exons |
| predict_jr_exon | Predict novel exons from reads with 2 junctions |
| predict_jrp_exon | Predict novel exons from read pairs with two splice junctions |
| prepare_annotation | Prepare anntation |
| sj_touching_exon | Determine which side of the splice junction touches an exon |
| transcript_range | Transcript range |
| upstream_count | Count mapped parts in a read from 1 to max (from 5' to 3') |
| which_exon_terminal | Determine terminal end of a splice junction |
