Hi, when I check the data after read_10x_vdj, I see multi_chain column shows false while extra_chains is filled with something like: [{“c_call”: “IGLC1”, “consensus_count”: 27, “d_call”: null, “duplicate_count”: 1, “j_call”: “IGLJ1”, “junction”: null, “junction_aa”: null, “locus”: null, “productive”: false, “v_call”: null}]
If I understood correctly, extra_chains should be blank if multi_chain is false. Could you explain this?
Only productive chains are counted towards multi_chain. The chain in your example is non-productive.
As a side note if you still have the extra_chains column, you are likely using an outdated version of scirpy. Consider upgrading to the latest version with an improved data structure.