Compatibility with Cell Ranger 6

[vladie0]

Dear developers,

the new release of cell ranger incooporated some changes in the annotation of the contig files.

contig csv header cell ranger 5.X:
barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id

contig csv header cell ranger 6.X
barcode is_cell contig_id high_confidence length chain v_gene d_gene j_gene c_gene full_length productive fwr1 fwr1_nt cdr1 cdr1_nt fwr2 fwr2_nt cdr2 cdr2_nt fwr3 fwr3_nt cdr3 cdr3_nt fwr4 fwr4_nt reads umis raw_clonotype_id raw_consensus_id exact_subclonotype_id

This implies that the import module is not populating some columns properly for cellranger 6.X files, would you be able to provide support for Cell Ranger 6.X?

[grst]

Hi @vladie0,

thanks for pointing that out, I'll look into it.
Shouldn't cellranger by now also output AIRR files? Have you tried those with read_airr?

Cheers,
Gregor

Note to self: example files are available at https://www.10xgenomics.com/resources/datasets/integrated-gex-and-vdj-analysis-of-connect-generated-library-from-mouse-pbmcs-

[grst]

Using the example files, the import works for me without error. So you would like scirpy to also import the additional columns (fwr_{1,2,3,4}{,_nt}, cdr_{1,2}{,_nt})? Or am I missing something different?

[naity]

Using the example files, the import works for me without error. So you would like scirpy to also import the additional columns (fwr_{1,2,3,4}{,_nt}, cdr_{1,2}{,_nt})? Or am I missing something different?

Yes, I agree it would be very useful to import cdr1 and cdr2 sequences as well.