PacBio 4mC Support

[jdakota1305]

Hi All, first wanted to thank you for developing this tool. I work in a lab that currently focuses on pathogenic species of bacteria that are associated with the microbiome of various tumors and are implied in potentially affecting tumorgenesis via host-pathogen interactions.

We are interested in mapping the methylome of our clinical specimens to their annotated genomes, so DNAModAnnot has been a godsend in many ways. We use PacBio platforms to determine methylation abundance and motif detection, but have many species that are seemingly more regulated by 4mC methylation than the more canonically abundant bacterial 6mA.

Would there be any interest on your side for supporting annotations of 4mC methylation in bacterial genomes? We have plenty of base modification data from our Sequel sequencing projects. Just to clarify, 4mC is detecting in the same manner as 6mA by using the kinetics information from the instrument.

[AlexisHardy]

Hi jdakota1305,

I did not test extensively 4mC modifications with DNAModAnnot. But DNAModAnnot has been designed to use different DNA modifications so you should be already able to study the 4mC methylation patterns in bacterial genomes with this package.
As input, both PacBio RSII and Sequel were tested and are compatible with DNAModAnnot.

If you have issues with 4mC analysis with DNAModAnnot, feel free to add more information and I will see if I can adjust the package.