search

agshumate / Liftoff

An accurate GFF3/GTF lift over pipeline
GNU General Public License v3.0
427 stars 52 forks source link

Overlapping exons #98

Open adysimon opened 2 years ago

adysimon commented 2 years ago

Hello,

Even with -overlap 0.0, Liftoff can generate overlapping exons (example : exon1 [400279 400378] exon2 [400378 400725]) How to avoid this ? Would it be possible to merge this kind of exons ?

Version 1.6.1

Thanks, Adeline

agshumate commented 2 years ago

Hi Adeline, The -overlap options only refers to allowing two different genes to overlap. Exons from the same gene are never allowed to overlap but as you pointed out here it is possible for them to be right next to each other. Currently liftoff does not merge these sort of exons but thats an improvement I can add in the future. perhaps a tool like AGAT (https://github.com/NBISweden/AGAT) would clean these up and merge them although I dont know for sure.

adysimon commented 2 years ago

Hi Alaina, Thanks for your answer. AGAT was able to resolve the problem and merged the exons, that's great Yes, it would be nice to merge these sort of exons in the future so that Liftoff directly generates a "cleaner" gff. Otherwise, the tool is super !

agshumate commented 2 years ago

great, i will keep this issue open until the merging is implemented in liftoff. Thanks!