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rnabioco / djvdj

An R package to analyze single-cell V(D)J data
https://rnabioco.github.io/djvdj
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import vdj break when clonotype id is NA #62

Closed aurelBZH closed 3 years ago

aurelBZH commented 3 years ago

Hi, Thanks for your great work on djvdj. I had some problem with the import function. When the clonotype id is NA the function don't concatenate the row, the function can't use barcode as metadata and break.

thanks a lot

sheridar commented 3 years ago

Thanks @aurelBZH, I was able to replicate the issue and will work on fixing this

sheridar commented 3 years ago

I adjusted the import function so it will ignore contigs that do not have a clonotype id. I have only encountered this issue in a dataset I started analyzing yesterday. In my recent dataset I found a contig that was classified as high_confidence, productive, full_length, and had the same CDR3 sequence as another contig assigned to the same cell. But this contig was not assigned a clonotype id.

It's not clear to me why this would occur, so I reached out to the 10x support staff to see if they could provide any insight.

If you re-install, the import function should now work, but the contigs that lack a clonotype id will be excluded from the data. Let me know if you have any questions/concerns or if you experience any further issues

aurelBZH commented 3 years ago

thanks a lot for your prompt response ! i close the issue