HELP with PacBio RS reads for epigenetics

Question

[sarajorqueraortega]

Hi Im working on my master's thesis. I'm new to bioinformatics and i and I'm fighting with differents tools to identify epigenetics in PacBio RS reads. I know my data is old, but its what i have so i need help about how to make the first process of my pipeline. I want to evaluate the quality of my reads (that i convert from bax.h5 to .bam) and filter them if necessary but i dont know what tools to use. Can anyone help me Thanks so much

[Billy Rowell]

There were workflows for identifying base modifications in microbial data generated on RS II, as highlighted in old decks like this.

Your best bet is to email [e-mail] and ask for pointers to the documentation for RS analysis. In your email:

• point to the source of your data
• ask where you can find the tools for converting bax to bam (bax2bam), assembling, and identifying base modifications
• ask for any documentation or guidance for these tools

Answer 1

[GenoMax]

PacBio has many video tutorials available: https://www.pacb.com/learn/resources/educational-videos/

They also make various workflows/pipelines available : https://github.com/PacificBiosciences

You can also reach out to support at pacb.com for assistance.

Past threads that may help:

Pulse information of PacBio data

Answer 2

[colindaven]

I don't think you can identify methylation in reads from a machine of that age - at least without 2000x coverage (not joking sadly). I believe the modern methylation calling was introduced with the Hifi or even Revio devices, but am not sure. I'm sure the pacbio bioinformaticians can give you a quick confirmation which minimum sequencer model was needed.

[sarajorqueraortega]

ou :( are data from WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations. Do you think PacBio's technical service will respond to me this week? Thank you so much

[colindaven]

No clue - I think this is their most modern methylation calling software, seems to require Hifi - https://github.com/mattoslmp/primrose