Can I run DESeq2 with SMART-Seq data

Can I run DESeq2 with SMART-Seq data

1

@assa-yeroslaviz-1597

Last seen 2 days ago

Germany

my data set comes from single-cell SMART-Seq data, where I have in total 48 samples, 24 samples for the control and 24 for my KO. Each sample represent one cell.

I have used STAR to map the samples against my indexed genome and featureCounts to quantify the reads onto the genes.

If I do a pre-filtering before running the DESeq function only very little genes are left, as I’m not sure what a meaningful filter threshold would be.

keep <- rowSums(counts(dds) <= 100 ) == 12
table(keep)

keep
FALSE  TRUE 
56869   141 

I was wondering if this is a feasible way of analysing the data, as I have many 0 reads in the count matrix (which would have been expected from the single-cell data set.

(or would the kallisto -> tximport -> DESeq2 or Kallisto -> RSEM way would be better in this case?)

thanks for the advice

Assa


DESeq2


SMART-seq

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