Question: MeDIP-seq and hMeDIP-seq analysis
gravatar for Grinch
3.6 years ago by
Grinch70 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 • 2.2k views
ADD COMMENTlink modified 3.6 years ago by dally180 • written 3.6 years ago by Grinch70
gravatar for dally
3.6 years ago by
United States
dally180 wrote:

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 3.6 years ago by dally180
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2114 users visited in the last hour