Question: MeDIP-seq and hMeDIP-seq analysis
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gravatar for Grinch
3.1 years ago by
Grinch30
Germany
Grinch30 wrote:

Hi! I'm analysing MeDIP-seq and hMeDIP-seq data for the first time (I've analysed ChIP-seq and RNA-seq data sets before) and was wondering if people who have done it before can recommend pipelines they have used and/or programmes for quantitative comparison of ChIP-Seq data. My data set is made of replicates and has 2 disease subtypes and healthy samples.

I've analysed with the new MethylAction pipeline and MACS peak caller, but to compare between the two I need to choose a programme for quantitative comparison for the peaks I get with MACS, so I can see which one gives me better results for my data.

If anyone has knowledge of a better pipeline, that would also be of use, but firstly I need to quantitate the peaks.

Thank you all!

chip-seq hmedip-seq medip-seq • 1.9k views
ADD COMMENTlink modified 3.1 years ago by dally170 • written 3.1 years ago by Grinch30
1
gravatar for dally
3.1 years ago by
dally170
United States
dally170 wrote:

https://ethanomics.wordpress.com/2014/02/19/medip-seq-data-analysis-diffreps/

This might at least get you looking in the right direction. I've used diffReps before and it's quite easy to work with.

ADD COMMENTlink written 3.1 years ago by dally170
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