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
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