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  • How to select batch correction features for single cell RNA seq?

    Hi All,
    I am new to computation and I have a total of 40 files [paired end] each ranging form 3 to 10 GB for two different datasets [same organism, embryonic stem cells, differ in small and large groups]. I am trying to find out which genes are expressed in these groups of cells.

    For that I have read some papers and got a pipeline the first step of which is to peform batch correction [using kBET and MNN]. The kBET method is asking for features/genes as columns and cells as rows for the matrix it takes. However, I am not sure where to obtain these genes from?

    Please help!!

    -Getan

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