I’m giving a course on repseq in Portugal, and I’d like just to use one pass of IgBLAST (rather than run migmap for vdjtools), then process the results in ChangeO and vdjtools. Matching up the fields, I have:
I’m assuming that CDR3nt is the CDR3_IMGT, and I can easily translate to get to the vdjtools CDR3aa. How does one go from Change-O to the Vend, Dstart, Dend, Jstart variables in vdjtools? I know it’s simple maths, but in my experience, 99% of bugs are due to indexing errors, and it looks a little fiddly.
In addition, it would also help in CDR3 analysis if these variables (Vstart, Dstart, Dend, Jstart) were added to the ChangeO format specification in some form, so naming is consistent.