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frattalab / PAPA

PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data
GNU General Public License v3.0
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Replace assembled first exons of matched novel transcripts with matching reference first exon #6

Closed SamBryce-Smith closed 1 year ago

SamBryce-Smith commented 3 years ago

As with 3'end, StringTie is likely not defining these very accurately (is fairly clear from manual browsing but I shouldn't jump to conclusions...)

As this is not a problem I'm trying to solve (defining novel 5'ends/TSS), it may be worth avoiding adding extra noise/variation/uncertainty by replacing the assembled first exons of novel events with the matching reference first exon.

Something to consider...

SamBryce-Smith commented 1 year ago

Closing as won't be reporting full transcript models as output, only the novel last exons