Question: How to connect htseq-count to DESeq2?
0
gravatar for scheme4193
18 months ago by
scheme419380
scheme419380 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
ADD COMMENTlink modified 18 months ago by h.mon32k • written 18 months ago by scheme419380
2
gravatar for h.mon
18 months ago by
h.mon32k
Brazil
h.mon32k 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 COMMENTlink written 18 months ago by h.mon32k

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 REPLYlink written 18 months ago by ATpoint44k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2568 users visited in the last hour
_