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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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About run Somatic SNV calling from scRNA-seq #16

Closed monoplasty closed 11 months ago

monoplasty commented 12 months ago

Hello, Thank you for developing such a wonderful method. I use single-cell sequencing data to run Somatic SNV calling from scRNA-seq, but I don't know how to prepare the cell barcode file. Because the barcode.tsv file produced by cellranger has only one column, and the csv file given in the case has 2 columns, I don’t know what the id in the second column means? How to prepare this file? Can a randomly generated non-repeating serial number be used?

Could you please provide some guidance on how to resolve this issue? Thank you in advance for your assistance.

jinzhuangdou commented 12 months ago

Hi the second column is the number of reads detected in the cell which could be from Seurat object. Thanks for your report. We have added this in README now

jinzhuangdou commented 12 months ago

You can select top N cells based on your own dataset