Gene abundance DESEq
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0
Entering edit mode
Vapin • 0
@dd8ababf
Last seen 20 hours ago
Germany

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 ?

DESeq2 • 150 views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States

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

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Entering edit mode
ATpoint ★ 1.6k
@atpoint-13662
Last seen 15 hours ago
Germany

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?