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Question: How to connect htseq-count to DESeq2?
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gravatar for scheme4193
18 months ago by
scheme4193 • 80
scheme4193 • 80 wrote:

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.
mapping deg rna-seq next-gen R • 1.4k views
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modified 18 months ago by h.mon ♦ 32k • written 18 months ago by scheme4193 • 80
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gravatar for h.mon
18 months ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k wrote:

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.
ADD COMMENT • link written 18 months ago by h.mon ♦ 32k

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.

ADD REPLY • link written 18 months ago by ATpoint ♦ 44k
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