something is wrong with VDJ recombinations

mandricigor / imrep

ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

https://mandricigor.github.io/imrep/

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Closed mandricigor closed 7 years ago

mandricigor commented 7 years ago

Hi Igor,

I think something is wrong with VDJ recombinations

for example

CDR3_AA_Seq Chain_type Read_count V_chains D_chains J_chains

CSSRRVYFLSDAAERGASTFVYW 4 IGH IGHV7 NA

CLGSHWPSGSGAPQAYDFDLVW 4 IGH IGHV7 NA

CSLPSHSLHILVGQLPGAFGVW 2 IGH IGHV7 NA

/u/home/s/serghei/scratch/BCRSEQ/imrep_final/imrep_009-0249.txt

There is not value for D and in the majority of cases J gene is missing