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gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
MIT License
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Transcript classification codes ? #74

Closed hmyh1202 closed 2 years ago

hmyh1202 commented 2 years ago

Hi，

which code is potentially novel isoform ?

Thank you.

gpertea commented 2 years ago

If you are looking for novel alternative splicing isoform (with novel junctions), code j might be the more "promissing" one. See the table at http://ccb.jhu.edu/software/stringtie/gffcompare.shtml#transfrag-class-codes However there are other codes that can potentially capture that - even k (reverse containment) or o (other unclassified overlap) could be revealed to be a novel isoform. Of course, transcriptional noise, alignment artifacts and even assembly issues (fragmentation, coverage bias etc.) should be considered.

One could argue that even code = (matching) could in fact hide a potentially novel isoform - one with a different TSS and/or TES, perhaps.

So the most disappointingly encompassing answer to your question could be: "all of them".