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Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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some Questions about the results #28

Closed shangguandong1996 closed 5 years ago

shangguandong1996 commented 5 years ago

Hi, Magdoll. I follow the Iso-Seq3 -> Cupcake ToFU -> SQATNI pipeline. I have some question about the sqanti result. First,I noticed the result in XX.collapsed.rep.renamed_corrected.gtf is like

transcript_id "PB.1.1"; gene_id "PB.1.1";

instead of 

transcript_id "PB.1.1"; gene_id "PB.1";

Second, I found no gtf output after I run sqanti_filter2.py although I can grep filterd gene in corrected.gtf to make filter.gtf.

Thanks for you pipeline. These are very helpful !

Magdoll commented 5 years ago

Hi @shangguandong1996 ,

The latest (v4.0) now outputs GTF with sqanti_filter2.py please give it a try.

Thanks, -Liz