Question: Analysing MIRA-seq methylation data
1
gravatar for Saad Khan
5.0 years ago by
Saad Khan330
United States
Saad Khan330 wrote:

Hi, 

I have a MIRA-seq data that I want to analyze. In the past I have used Bisulfite data for methylation analysis. There are a number of options available for Bisulfite data (e.g. aligners e.t.c. Aligning with Bismark etc and downstream analysis with methylkit/methpipe e.t.c.) I want to know what are the options or pipeline available for MIRA-seq data. Also what are the best practices for DNA methylation analysis with MIRA-seq.

ADD COMMENTlink modified 5.0 years ago by Charles Warden6.6k • written 5.0 years ago by Saad Khan330
0
gravatar for Charles Warden
5.0 years ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

MIRA is a MeDIP-based strategy.  In general, you'll want to use a normal aligner (such as BWA or Bowtie) and a ChIP-Seq/ChIP-chip peak-calling algorithm (MATS, MACS, etc.).  I've used MATS on MIRA tiling array data, but I can't absolutely promise that is the best strategy.

ADD COMMENTlink written 5.0 years ago by Charles Warden6.6k

Can MEDIPS be used for the same purpose or do we have to use MACS/MATS?

Thanks

ADD REPLYlink written 4.7 years ago by smk30

I haven't tried it, but I Googled the MEDIPS Bioconductor package and I think it looks appropriate.  There are lots of valid peak calling algorithms out there - I just think MATS/MACS are the most commonly used.

ADD REPLYlink written 4.7 years ago by Charles Warden6.6k

How do you do differential methylation analysis once you do peak calling with MATS/MACS

ADD REPLYlink written 4.7 years ago by smk30

The peak calling compares the signal between the two groups (which perhaps has been normalized against an input reference). So, peaks called due to a significant difference in signal between the groups are most likely to be differentially methylated.

ADD REPLYlink written 4.7 years ago by Charles Warden6.6k
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