Hi all,

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 ?

You shouldn't use TPM or FPKM with DESeq2. And low TPM or FPKM values are probably not materially different from a zero anyway.

I do not see the point using stringtie here. DESeq2 can give you proper FPKMs but you have to give it information about the gene length. This should come at best from a method that accurately determines it, such as salmon, or from the htseq output. Then you can either use the dedicated DESeq2::fpkm function or calculate TPMs manually as shown here: DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?