ablab
antisense classification for ONT direct RNAseq data
Hello,
First of all thank you for designing this tool. So far it has very useful on my datasets.
With enable the --sqanti_output parameter, I obtained the SQANTI3-like format data for isoform classification.
But, I can not get the antisense type for identified isoforms. In my mind, ONT direct RNAseq were strandness sequencing, it can identify the antisense isoform type.
Could you clarify why does not exist the antisense isoform in my data ?
Thank you in advance!
Bai,
Dear @baishengjun
Sorry for the delayed response and thanks for the feedback.
At the moment IsoQuant does not exploit dRNA properties fully. Currently, when stranded data is provided only minimap settings are changed to ensure reads are mapped correctly. Unfortunately, detection of antisense transcripts is not implemented yet, but is on our roadmap and might appear in some of the next releases. Sorry to bring this news.
Best Andrey
This would be really useful... any ideas on when this will be released?
@rebeelouise
Unfortunately, I am the only one currently working on IsoQuant. It's very hard to predict current timeline considering other ongoing research projects. I really hope I can get my hands on it.
Best Andrey
@rebeelouise
Unfortunately, I am the only one currently working on IsoQuant. It's very hard to predict current timeline considering other ongoing research projects. I really hope I can get my hands on it.
Best
Andrey
Hi again!
Well all of the best! Again this would also be a very useful feature for a virologist like me! Happy to chat if helpful!
Best,
Rebee :)