How to connect htseq-count to DESeq2?
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2.2 years ago
takoyaki ▴ 90

I want to know how to use htseq-count data for detecting DEGs by DESeq2.

We can get gene expression count matrix by htseq-count, and also we can use this output in DESeq2. However, the last 4 rows of htseq-count matrix are not count data but information about counting result.

Do everyone remove last 4 rows by themselves in R ?

Or are there any functions in DESeq2 to pass the raw result of htseq-count ?

So, in conclusion, I want to know how to connect htseq-count to DESeq2. Thank you.

R RNA-Seq next-gen DEG Mapping • 2.2k views
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HI,

I have two separate matrix for normal and control. DeSeq2fromHTSeqcount , may i have to run separately for each matrix. I want GE.txt for further analysis. Please help me to input the data in Deseq2

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2.2 years ago
h.mon 33k

Or are there any functions in DESeq2 to pass the raw result of htseq-count ?

Yes, there is a function called DESeqDataSetFromHTSeqCount(). You can read about it in a section of the manual titled htseq-count input.

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scheme4193, DESeq2 exists for quite a while now, the manual is outstandingly comprehensive. Please read it carefully, you'll find answers there, starting from input preparations over design formulas etc and troubleshooting.

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