Implement distance constraint for AP, AT events

ajw2329 / junctionCounts

Utils for identifying pairwise alternative splicing events and quantifying them using junction reads.

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Implement distance constraint for AP, AT events #2

Closed ajw2329 closed 6 years ago

ajw2329 commented 6 years ago

Currently alternative polyadenylation/alt-TSS events are specified by two exons with the same inner coordinate (splice site) but different outer coordinates. The outer coordinates can differ by as little as 1 nt. This most likely allows for many false positives, particularly when input GTFs come from transcriptome assemblers.

ajw2329 commented 6 years ago

Distance constraint implemented with default of 100 nt.