Question: DESeq2 input for PE data (Raw count-pairs or 2 x Raw count-pairs)
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gravatar for xfwang
4.2 years ago by
xfwang20
United States
xfwang20 wrote:

Dear there,

I know DESeq2 expects raw read counts as the inputs which is important for DESeq2's statistical model to hold (it has been emphasized many many times).

For singed-end reads, the counts should be the number of reads mapped to the gene. But, how about paired-end data, is it the number of mapped reads or fragments to the gene?

In another word, do I need to multiple 2 for the counts from htseq-count for PE data because htseq-count count reads pairs for PE data?

Thank you so much!

Best,

Xiaofei

 

 

 

deseq2 • 601 views
ADD COMMENTlink modified 4.2 years ago by Ryan C. Thompson7.4k • written 4.2 years ago by xfwang20
Answer: DESeq2 input for PE data (Raw count-pairs or 2 x Raw count-pairs)
0
gravatar for Ryan C. Thompson
4.2 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.4k wrote:

No, use the counts of overlapping fragments. Each fragment is one observation of a gene, regardless of how many reads were produced from that one fragment.

ADD COMMENTlink written 4.2 years ago by Ryan C. Thompson7.4k

Thanks a lot!

ADD REPLYlink written 4.2 years ago by xfwang20
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