DESeq2: possible to compare read counts at single nucleotide level ?
2
0
Entering edit mode
bioinfo • 0
@bioinfo-12782
Last seen 3 months ago
United States

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 ?

deseq2 rnaseq • 475 views
ADD COMMENT
3
Entering edit mode
@mikelove
Last seen 3 days ago
United States

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 COMMENT
0
Entering edit mode

Thanks for your help !!

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
@gordon-smyth
Last seen 34 minutes ago
WEHI, Melbourne, Australia

See the derfinder package.

ADD COMMENT

Login before adding your answer.

Traffic: 190 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6