Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
Hi,
I would like to use SoupX for ambient RNA removal. However, I am using barcode-gene matrix datasets downloaded from NCBI GEO which don't always include raw data. Can I still use SoupX without the raw barcode-gene matrix?
Thanks and good day.
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malonzm1 •
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No, it will not work without raw counts (
tod).SoupXrequires requires table of counts (toc) and pass that along with the raw counts (tod) to createSoupChannelwhich will be used to estimate what the expression profile of the soup.Many thanks.