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robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool
qb.cshl.edu/ginkgo
BSD 2-Clause "Simplified" License
47 stars 28 forks source link

The input file format #39

Closed biowumin closed 2 years ago

biowumin commented 2 years ago

Hi, thank you for providing this tool for CNV analysis. I want to use ginkgo to infer CNV of single cells, and I wonder the input files format, that is, the bed file and the FACS file. One bed file contains one cell? Can you provide an example? Thank you so much!

robertaboukhalil commented 2 years ago

That's right, 1 bed file = 1 cell. You'll find instructions on what those bed files should look like/how to generate them on the sidebar at http://qb.cshl.edu/ginkgo, under "Help". As for the FACS file, the format is a tab-separated file with 2 columns: the cell name, and the estimated ploidy.