I have performed a DESEq analysis from Htseq count data as follows.
ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition) dds<-ddsHTSeq dds <- DESeq(dds, quiet = T)
Then I used String Tie for the abundance. But I found some genes with low TPM and FPKM values in String Tie output where the HTseq count says Zero. So my question which option I can use to get TPM and FPKM in DESEq per samples ?