pacificbiosciences/methbat

A battery of methylation tools for PacBio HiFi reads

MethBat : A battery of methylation tools for PacBio HiFi reads

MethBat will aggregate and analyze CpG methylation calls made from PacBio HiFi datasets. Key features include:

• Creation of a methylation profile for a collection of genomic regions (e.g., CpG islands)
• Creation of cohort / background profiles from a collection of methylation profiles
• Analysis of cohort profiles comparing sub-groups (e.g., case v. control, male v. female)
• Segmentation of the CpGs in a dataset into Methylated, Unmethylated, or ASM regions

Authors: Matt Holt, Chris Saunders

Early release warning

Please note that MethBat is still in early development. We are still tweaking the input / output file formats and making changes that can affect the behavior of the program.

Availability

• Latest release with binary

Documentation

• Installation instructions
• User guide with quickstart
• Output files
• Methods
• Data files

Citation

MethBat does not currently have a pre-print or publication.

Need help?

If you notice any missing features, bugs, or need assistance with analyzing the output of MethBat, please don't hesitate to open a GitHub issue.

Support information

MethBat is a pre-release software intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that MethBat lives up to the quality that PacBio strives for, we make no warranty regarding this software.

As MethBat is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any MethBat release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.

DISCLAIMER

THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

methbat's Issues

input regions

methbat profile
--input-prefix {IN_PREFIX}
--input-regions {IN_REGIONS}
--output-region-profile {OUT_PROFILE}

How would I get the input regions for a non-model organism not available on UCSC browser tables?

About metagenomic data

Hi,

Thank you for implementing this great tool.

I am trying to use this tool to get methylation profile for my metagenomic data, but I got the error:

[2024-05-26T17:07:43.378Z ERROR methbat] Error while verifying settings: hap1_bed does not exist: "ref_pbmm2_6G_len_1000.hap1.bed"

pb-CpG-tool does not generate hap1 adn hap2 file as it is metagenomic data. But I still wonder can we use this tool to ge methylation profile?

Best,
Jin

data available

Hi

I'd like to inquire whether the input for the program should be 'subread.bam' or a BAM file processed through CCS? And is there any sample data available for testing purposes?

Best
Zhongyu