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Comparing bisulfite sequencing data to non-bisulfite sequencing data and infer methylation sites?

Hi all,

I have recently started looking into how to analyze bisulfite sequencing data, which I am completely new to, and am hoping if someone here could provide some insights.

I work on a non-model species, and I have whole genome sequencing data of bisulfite converted DNA (WGBS), as well as whole genome sequencing of non-converted DNA (WGS) obtained from the same set of samples. The goal is to identify methylated regions by comparing these two types of data.

Does anyone know if there are any tools out there that consider both WGBS and WGS and infer methylated sites? As far as I know, many tools like Methylkit only consider only WGBS data, and I wasn't sure if this is something that is done by custom made scripts or if there are any existing tools out there I could use.

Many thanks in advance!

Miyako

bisulfite sequencing wgbs methylation wgs
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written by miyakokodama • miyakokodama

I do not see why you need non-converted DNA. This does not add any information towards methylation. WGBS will give you the information you want. Bismark is a standard tool/pipeline for alignment of WGBS to an in-silico bisulfite converted genome followed by methalation calling: https://www.bioinformatics.babraham.ac.uk/projects/bismark/

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written by ATpoint ATpoint

Would you mind elaborating on that a bit?

We don't know the bisulfite conversion rate (the libraries were not spiked with phage genome), and incomplete bisulfite conversion would be a problem. That being said, potential bisulfite failure, sequence variation and misalignment could lead to errors calling methylation sites, hence comparison of methylated regions to the genome would be beneficial?

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written by miyakokodama • miyakokodama

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