How to find UMI counts from cell ranger VDJ output
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12 weeks ago
Kevin ▴ 50

I ran cell ranger multi with VDJ and cell surface samples and the results look good. I have not been able to find info on UMI counts for IgH, IgL, or IgK and was wondering if there is a specific file I should be looking in? Would they have needed to be included in the feature barcode csv as part of cell rangers input?

cellranger • 258 views
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13 days ago
mizraelson ▴ 60

hi, I would also suggest using MiXCR for 10x vdj data analysis. There is a single line command for that:

mixcr analyze 10x-vdj-bcr \
 --species hsa \
 sample_R1.fastq.gz \
 sample_R2.fastq.gz \
 sample_result

As the result you will get several files, the tsv file will have all the info for every clone (cell barcode, umi barcode, cdr3 sequence, etc.)

You can read more on it here: https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10xgenomics

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