Gene abundance DESEq
2
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
ADD COMMENT
1
Entering edit mode
@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.

1
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?

ADD COMMENT

Login before adding your answer.

Traffic: 307 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6