Issue with Extracting Light-Kappa Chains in Dog

[MikolajKocikowski]

Hi,

I've been using the imgt.202312-3.sv8.json germline database with the latest MiXCR (Oxford Nanopore preset) for extracting heavy and light chains from dog samples. While I've successfully extracted heavy and light-lambda chains, I encountered issues with light-kappa chains. Specifically, of the 10 samples, only one produced a light-kappa file, containing a minimal number of sequences (one or two), which seems like an artifact. Given that some of the sequenced samples are known to contain kappa chains, this result is unexpected.

I'm looking for the culprit behind the lack of kappa chains. Any advice would be greatly appreciated, thanks!

[mizraelson]

Hi, can you share the align report for the sample where you expect the missing chain?

[MikolajKocikowski]

Hi! I attach two files from samples known to contain kappas among other chains. Barcode09 file produced the IGK output file with one chain, Barcode10 did not. Moderate alignment success rate is expected due to the nature of the library. Samples contain scFvs and some single chain constructs. Thanks for taking a look!

barcode09_result.align.report.txt
barcode10_result.align.report.txt

[mizraelson]

I see, well the successfully aligned reads rate is rather low indeed here. Is it possible to identify a read that covers IGK from the the original FASTQ file but appears not to be aligned correctly?