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spond / IgSCUEAL

B-cell 454 processing
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IGH-Full reference does not annotate by D region #11

Closed sdwfrost closed 9 years ago

sdwfrost commented 9 years ago

Dear @spond ,

My bad, I'm sure, but the IGH-full reference alignment doesn't annotate the D regions properly.

spond commented 9 years ago

Hi @sdwfrost,

My bad, actually. The MergeVRegionsAlignments.bf was (incorrectly) auto-detecting CDR3 as a nucleotide alignment, and skipping (silently) it from the merge operation. This makes the reference alignment for HumanIGH_full broken (no CDR3) and causes downstream files (which assume non-empty entries for each of the FR and CDR regions) to return silly results.

IMGT times out today when I try to pull down their alignments, otherwise I would rebuild IGH_full. You can use commit a0c5971ca01b702dfb55087ea6ae34ae6f672e1c to try rebuilding yourself, or you can send me the nucleotide sequences for IGH.

Sergei

sdwfrost commented 9 years ago

Dear @spond , thanks, I'll send along the files.

spond commented 9 years ago

Resolved with 4cece00f98ed4a7c08ec9567bbc0633a368db8c6