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Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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gene_id annotation #55

Closed morellr closed 4 years ago

morellr commented 4 years ago

sqanti_qc2 (v.7.3.2) no longer substitutes overlapping gene_id from the reference annotation gtf in the the gene_id field of the .collapsed.gff file -- they all are "PB.". It is very helpful to have this annotation, could you please restore this function?

Also, if the annotated gene_id field could be propagated to the *.filtered_lite.gtf created by sqanti_filter2, that would be great also!

morellr commented 4 years ago

I should have been clearer: in previous versions a *.renamed_corrected.gtf.cds.gff was produced that used overlapping gene names from the reference gtf as the gene_id. In v.7.3.2, this file is not made.

morellr commented 4 years ago

Embarassing. I see now that the equivalent output is made in v.7.3.2 -- just the naming convention is different. Now this file is *rep_corrected.gtf Sorry for the confusion.