search

mortazavilab / TranscriptClean

Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
MIT License
65 stars 17 forks source link

TODO: Implement function in transcript2 class to compute jM and jI sam fields #1

Closed dewyman closed 6 years ago

dewyman commented 6 years ago

Output sam files from the STARlong aligner contain two custom tags (jM and jI) that describe whether each splice junction is canonical and where each intron begins and ends. TranscriptClean uses these tags when correcting noncanonical splice junctions. However, not everyone can use STARlong to align their transcripts. Computing the jM and jI fields directly in my script would expand the splice junction correction feature to more people.

dewyman commented 6 years ago

This functionality has been implemented and tested.