Coverage and identify information for mRNAs

[gemygk]

Hi @agshumate

I appreciate you and your team's effort for developing the tool Liftoff.

Having used liftoff versions (v1.1.3, 1.3.0 and 1.4.2), I could see in the output.gff file generated by liftoff that the gene type contains coverage (-a) and identity (-s) information provided as coverage=1.0;sequence_ID=1.0 in the attribute field. I believe this is a cumulative coverage across all the mRNAs of a gene.

Is it possible to have same information added to the mRNA type as well, i.e. to have coverage=?;sequence_ID=? for each mRNA that was transferred across. This will enable users to run Liftoff with the default coverage and identify cutoff of 0.5 and then easily workout those mRNA's that were 100% transferred within a gene and those that weren't transferred at 100%.

I am yet to test the latest release v1.5.1. Apologies if this feature is already added.

Thanks,
Gemy

[agshumate]

Hi Gemy,
It is correct that this is a cumulative coverage and this is the case in v1.5.1 as well. I agree that will be useful to add for mRNA as well so I can add that in a future release.
Thanks!
-Alaina

[gemygk]

Thanks, Alaina. Please close this ticket after you make the changes.

Best,
Gemy

PS: Alaina is my daughter's name too!

[tomasbruna]

Hi @agshumate,

any progress on this? I'd also be interested in the feature.

Thanks!
Tomas