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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Barcodes File Clarification #81

Closed DarioS closed 1 year ago

DarioS commented 1 year ago

In the documentation, I see -b $BARCODE but it doesn't explain what is required file format nor where to download it for Chromium.

hxj5 commented 1 year ago

Hi, -b requires a file listing cell barcodes, one barcode per line. You may use the barcodes.tsv file in the output directory of 10x CellRanger, outs/filtered_gene_bc_matrices/.

DarioS commented 1 year ago

That's useful to know. Could you add it to the user manual so that it also helps others with the same confusion?

hxj5 commented 1 year ago

yes sure, thanks for your suggestion.

EDIT: commit be55773