Barcode whitelist in seurat

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2.5 years ago

ahmad mousavi ▴ 800

Hello,

I am wondering if anyone know where can I found the barcode whitelist in Seurat?

I need this barcode_whitelist.tsv for my analysis but I could not found in Seurat website.

thanks.

scRNA ngs scRNA-seq • 644 views

ADD COMMENT • link updated 2.5 years ago by cpad0112 21k • written 2.5 years ago by ahmad mousavi ▴ 800

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see if this post works for you: RNA-Seq Cell Barcode Whitelist 10X. An R package exists for https://rdrr.io/github/compbiomed/scuff/man/validCb.html for 3' v2, 5' v1 and v2, 5' HT v2 of 10x. You can follow this link to find the list of barcodes used for various 10x experiments: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist-. A few, you can download from here: https://github.com/10XGenomics/cellranger/tree/master/lib/python/cellranger/barcodes. You can also identify approximate list of true barcodes using this method: https://umi-tools.readthedocs.io/en/latest/reference/whitelist.html. Please post the technology you have used in experiments.

ADD REPLY • link 2.5 years ago by cpad0112 21k

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