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Question: DESeq2: possible to compare read counts at single nucleotide level ?
0
gravatar for bioinfo
7 months ago by
bioinfo0
bioinfo0 wrote:

Hi, I have some candidate genomic regions of interest and would like to see if they are differentially expressed between two conditions. Each condition has three biological replicates.

Because I cannot define the boundaries of the candidate genomic regions exactly (they are not annotated with gene model), I thought about comparison read counts at the single nucleotide level (therefore comparison of sequencing depth) and applying some thresholds (p-value or test statistics) to define differential (continuous) regions. Is it possible for me to provide DESeq2 with read counts at single nucleotide resolution ("depth") to perform statistical tests generating statistic or p-value so that I can get significant at each base ?

rnaseq deseq2 • 206 views
ADD COMMENTlink modified 7 months ago by Gordon Smyth36k • written 7 months ago by bioinfo0
Answer: DESeq2: possible to compare read counts at single nucleotide level ?
3
gravatar for Michael Love
7 months ago by
Michael Love22k
United States
Michael Love22k wrote:

I would not recommend running DESeq2 on read depth in regions. The dispersion estimation may be thrown off and the multiple test correction needs to be considered as you have very high correlations for each position with neighbors.

ADD COMMENTlink written 7 months ago by Michael Love22k

Thanks for your help !!

ADD REPLYlink written 7 months ago by bioinfo0

By the way, when ChIP-seq data is analyzed by DESeq2 for differential binding (for example: diffBind), the region is pre-defined by peak calling software such as MACS. Here, the size of region is variable. If read depth is not good for DESeq2, do you think that small size of region is also not good for DESeq analysis? Do you have any suggestion for minimum size of region good for DESeq2 ?

ADD REPLYlink written 7 months ago by bioinfo0

I don’t have much suggestion for this but my concern was driven by the auto correlation more than the range of counts.

ADD REPLYlink written 7 months ago by Michael Love22k
Answer: DESeq2: possible to compare read counts at single nucleotide level ?
0
gravatar for Gordon Smyth
7 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:

See the derfinder package.

ADD COMMENTlink written 7 months ago by Gordon Smyth36k
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