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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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CNV express all gene position of chromsome problem #600

Open dajunlee opened 1 year ago

dajunlee commented 1 year ago

Hi, I'm trying to troubleshoot the problem that cnv express all gene position of each chromosome. Let me know how to solve this problem. My data is from BD rhapsody libraries, could this be the issue? I'll share the png file.

Thanks, Jun

image
GeorgescuC commented 10 months ago

Hi @dajunlee ,

I am not familiar with BD rhapsody data, but looking at the figure, I think the issue might be related to the expression level and expression threshold for filtering. This type of result tends to happen when too many genes are filtered out. I would look at the average counts per gene (for example, plot the sorted average expression per gene across all genes) to determine what a good threshold value is and rerun infercnv using that new cutoff value.

Regards, Christophe.