PacBio methylation information in bam file

Question

[gabri]

Hi All,

I have some PacBio data in bam format obtained from the Sequel platform.

I know that the PacBio sequencing is able to captures the methylation information, but I don't know how to "obtain" these information.

Is there a way to know which bases in the bam files are methylated using samtools?

Or is there a compleatly different way?

Thank You

[GenoMax]

Was this data specifically obtained with that aim in mind?

There are a few requirements noted in this Tech Note and an older White Paper for methylation analysis.

You will need to use PacBio SMRTAnalysis software to do the analysis. Tutorials for base modification are linked on this page.

[gabri]

No these data were obtained for an assembly purpose. In fact I was not sure if the methylation information was included by default in the bam files. So probably it is not.

[gabri]

Ok thank you very much! I'll take a look.

Answer 1

[tjduncan]

I have complied some of the steps to do this in a previous post. I am not an expert on this by any means but most of PacBio's official documentation for this type of pipeline is outlined in the post linked below:

A: PacBio interpulse duration (IPD) data