Question: Relationship between histone marks and expression level inferred by ChIP-seq and RNA-seq
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2.1 years ago by
ch8316f5eyu10 wrote:

For example, I have samples sequenced both H3K27me3 and RNA-seq at 10 time point, and I want to see wether the expression level of genes is in negative correlation with H3K27me3 level. Is there a public accepted method? The way I adopt is that I treat the H3K27me3 sample as RNA-seq to calculate its CPM and the Pearson coefficient with CPM from RNA-seq. But this way completely ignore the peak concept which is important to ChIP-seq. Is there any better method?

rna-seq chip-seq gene • 638 views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan90k • written 2.1 years ago by ch8316f5eyu10
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

There nothing really wrong with what you're doing and I see ignoring the concept of peaks as a benefit. You might additionally do some clustering to see if there are subsets of genes that positively and others that negatively correlate (using deepTools, computeMatrix individually on the RNAseq and ChIPseq datasets, merge them together with computeMatrixOperations, and then cluster with plotHeatmap). But really, if it's obvious on the scatter plot of the CPMs then any method will show it.

ADD COMMENTlink written 2.1 years ago by Devon Ryan90k

Thanks for your reply. I am confused because I could not find any paper use this method. :)

ADD REPLYlink written 2.1 years ago by ch8316f5eyu10
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