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agshumate / Liftoff

An accurate GFF3/GTF lift over pipeline
GNU General Public License v3.0
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Coverage and identify information for mRNAs #50

Open gemygk opened 3 years ago

gemygk commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

Best, Gemy

PS: Alaina is my daughter's name too!

tomasbruna commented 1 year ago

Hi @agshumate,

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

Thanks! Tomas