Suitability of 'expected counts' from Smart-seq2 RSEM analysis as input for SCENIC #87
Description
Hi Aerts Lab,
I hope to analyse public single cell data from a PDOX medulloblastoma model that was sequenced on Smart-seq2 using pySCENIC. The data the authors deposited in NCBI GEO contains floating point values consistent with processed data rather than integer ‘raw’ counts so, to the best of my knowledge that can't be used as input for the initial step of the SCENIC workflow. When I enquired directly with them they stated they performed RNA-Seq by Expectation Maximization (RSEM) analysis ("expected counts from the RSEM analysis" are available). Could you please advise whether the expected count data can be used as input for the SCENIC pipeline?
Thanks in advance.