Total number of reads mapped to CDR3

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 smangul1 closed 7 years ago

smangul1 commented 7 years ago

Can you please report total number of reads mapped to CDR3 per chain besides unique CDR3

Also i still don't see the flag for chain type

Now it is hard to extract only CDR3 of certain type

Given the flag , we can do this

awk '{if($5=="IGH") print }'

Does it makes sense?

mandricigor commented 7 years ago

Please, explain what kind of flag. For the chain type? We have not discussed this yet, so why "still"....

smangul1 commented 7 years ago

I though we discussed long time agao Anyways just a flag= IGH,IGK, etc

right now the only way to extract certain chain is by grep which is not the best way just make field 2 to be this flag

mandricigor commented 7 years ago

Updated