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@maschon0 maschon0 released this 01 Jun 11:43
· 13 commits to master since this release
v1.1.1
ae15f57

Bugfix to v1.1.0 that irons out problems encountered in bookend elr when splice junction evidence is provided from multiple sources.

Splice junction evidence hierarchy:

  1. A reference splice junction database. This includes all splice junctions provided by an annotation file (BED12/GTF/GFF3) by the argument --reference, and/or all introns from a BED6 or STAR SJ.out.tab file provided by --splice. These are treated as maximally reliable, and an unannotated junction that is --sj_shift or fewer nucleotides away will be shifted to match the SJDB junction.
  2. Genomic motif, if a --genome is provided. The intron boundaries are checked for a strand-specific canonical or semi-canonical motif. Accepted motifs: GT-AG, GC-AG, AT-AC, GA-AG for forward-stranded alignments, and CT-AC, CT-GC GT-AT, CT-TC for reverse-stranded alignments.
  3. 'XS' and 'ts' tags passed from aligners. These are specific to the alignment settings of STAR/Hisat/minimap, so they can be of variable confidence.
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