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Question: DESeq2: possible to compare read counts at single nucleotide level ?
0
gravatar for bioinfo
13 days 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 ?

ADD COMMENTlink modified 7 days ago by Gordon Smyth34k • written 13 days ago by bioinfo0
3
gravatar for Michael Love
13 days ago by
Michael Love18k
United States
Michael Love18k 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 13 days ago by Michael Love18k

Thanks for your help !!

ADD REPLYlink written 13 days 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 11 days 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 11 days ago by Michael Love18k
0
gravatar for Gordon Smyth
7 days ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

See the derfinder package.

ADD COMMENTlink written 7 days ago by Gordon Smyth34k
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