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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

Using Ginkgo on a cell by bin matrix #29

Closed pedrofale closed 4 years ago

pedrofale commented 4 years ago

I would like to use Ginkgo to call copy numbers from data obtained with the 10X Genomics CNV solution, which outputs a cell by genomic bin matrix of (GC and mappability-normalized) read counts. However, your interface only seems to accept BED files as input. How would I go about applying Ginkgo to my matrix?

robertaboukhalil commented 4 years ago

Unfortunately, that's not supported, but in principle, you could run some of the code in process.R, starting at the segmentation step. Hope this helps!

vleblanc commented 4 years ago

Hi @pedrofale - I thought I'd chime in here since I've done the same thing you're trying to do (well, sort of). I made individual bam files for each cell using cellranger-dna bamslice (it's meant for pulling out groups of cells, but you can make it pull out individual cells easily enough), then made bed files from those and ran them through Ginkgo. I got reasonably similar results from both approaches. Hope this helps!

robertaboukhalil commented 4 years ago

Very cool, thanks @vleblanc!

pedrofale commented 4 years ago

Thank you, @vleblanc!