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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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faded out signal #440

Open msherafatian opened 2 years ago

msherafatian commented 2 years ago

Hi Thank you for providing this package and helping with resolving the issues. My question is in regard to weaker signals. I see that most of the tumour subclusters show clear strong CNVs in some regions but the same regions have weaker (faded out) signals in rest of the subclusters. Do you have any thoughts on the reason for this faded out signal. I expect CNVs to be binary, how should I interpret the faded out signals?

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mmfalco commented 2 years ago

Did you check the nCounts for those cells? Normally this happens to me when I have a subset of cells with lower library depth

msherafatian commented 2 years ago

Thanks for your quick response. That is indeed the case. They have the lowest nCounts.