Question: Correlation between gene expression (RNAseq) and RRBS methylation data
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gravatar for rahel14350
4 months ago by
rahel1435030
United States
rahel1435030 wrote:

Dear all,

I have data from gene expression (RNAseq) and RRBS methylation data from mm10. I would like to calculate the Correlation between this data. There are many packages for TCGA data but they didn't work on my data. Do you know any other packages work on RRBS and RNAseq data?

Kind Regards, Rahel

ADD COMMENTlink modified 4 months ago by i.sudbery8.2k • written 4 months ago by rahel1435030

they didn't work on my data

What was the problem? Please be more specific.

ADD REPLYlink written 4 months ago by ATpoint36k

The main reason is that they (for example TCGAvisualize_starburst in TCGAbiolinks or COHCAP package) are for array data such as EPIC, 450K or 27K.

ADD REPLYlink modified 4 months ago • written 4 months ago by rahel1435030
0
gravatar for i.sudbery
4 months ago by
i.sudbery8.2k
Sheffield, UK
i.sudbery8.2k wrote:

Try inTAD. While this is often used for correlating ATAC-seq with RNA-seq, I think the data in the tutorial is actually methylation data. I certainly don't see any reason it wouldn't work.

ADD COMMENTlink written 4 months ago by i.sudbery8.2k

Well it is not quite the same (if I am correct) because in RRBS we have methylation value for each single site but in ATACseq we have the coverage for each peak region. I might can adapt it by using only the DMRs but then what will be the methylation value for each sample? the mean or median of all sites in the DMRs?

ADD REPLYlink written 4 months ago by rahel1435030

How about taking the DMRs and looking at the average % methylation across them?

ADD REPLYlink written 4 months ago by i.sudbery8.2k

How about taking the DMRs and looking at the average % methylation across them?

ADD REPLYlink written 4 months ago by i.sudbery8.2k
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