Are There Any Tools For Finding Methylation Status Of Promoter Region?

Question

[samsara]

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 ?

Answer 1

[Ian]

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.

[samsara]

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

Answer 2

[Charles Warden]

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/

[samsara]

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

[Charles Warden]

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.