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AIRR Community Data Standards
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IGHD reading frame in AIRR format IgBlast output #626

Closed chunleya closed 1 year ago

chunleya commented 2 years ago

Jason, thank you for your time addressing this issue. I don't want to clutter up this channel with these questions so will make this the last.

I don't see how you can extract the D-reading frame from the D_germline_start without knowledge of the 3' junction. Perhaps D_CIGAR would help although i don't recognise its annotation from IgBlast. I'm sure i can write an R script to work RFs out but not sure which info to use from the IgBlast output. It would be easier if all the J-germline sequences started in the same frame but they don't.

Any pointers from anyone would be much appreciated

Regards

Harry White, Babraham Institute, Cambridge, UK

scharch commented 1 year ago

d_frame was added as an optional field in v1.4.1 WRT IgBlast specifically, it appears to have been added in release 1.23.0