Question: Are There Any Tools For Finding Methylation Status Of Promoter Region?
1
gravatar for samsara
6.7 years ago by
samsara600
The Earth
samsara600 wrote:

I have have data from RRBS (Reduced representation bisulfite sequencing). I have already mapped fastq files using Bismark. I have never worked with RRBS data, therefore got little lost.

What are the tools options for finding methylation status of promoter region? Are there any widely used pipelines for this ?

promoter methylation • 3.7k views
ADD COMMENTlink modified 6.7 years ago by Ian5.7k • written 6.7 years ago by samsara600
5
gravatar for Ian
6.7 years ago by
Ian5.7k
University of Manchester, UK
Ian5.7k wrote:

I have been using Bismark on SureSelect CpG regions (BS-seq). My pipeline used 'bismark' to map, followed by 'bismark_extract' to call methylation. Whilst looking for RRBS information I found the following document specifically referring to RRBS: http://www.bioinformatics.babraham.ac.uk/projects/bismark/RRBS_Guide.pdf

Then, as cwarden45 says (+1), I would use methylKit. You can look in specific regions as well using:

reads=read.bismark(...)
promoters = read.bed("promoter_coordinates.bed", remove.unusual=TRUE)
reads_in_promoters = regionCounts(reads, promoters)

I hope this helps.

ADD COMMENTlink written 6.7 years ago by Ian5.7k

it really helped. One more query, where can i find mm10 promoter sequences bed file ?

ADD REPLYlink written 6.7 years ago by samsara600
3
gravatar for Charles Warden
6.7 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

You can use methylKit to identify differentially methylated regions, and I believe the annotate.WithGenicParts() can help you find the subset in promoter regions:

https://code.google.com/p/methylkit/

ADD COMMENTlink written 6.7 years ago by Charles Warden7.8k

Before methylKit, i need to perform methylation call. Which is mostly used methylation call software?

ADD REPLYlink written 6.7 years ago by samsara600

Yes - I would recommend using the extended Bismark pipeline. The goal should be to produce .bed files with percentage methylation values.

I have some Perl script templates that you might be able to use here:

https://sites.google.com/site/cwarden45/scripts

However, this requires you know how to read the Perl script. Otherwise, I would recommend reading the user manual for Bismark.

ADD REPLYlink written 6.7 years ago by Charles Warden7.8k
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