Feature request: support for 4mC motifs with new models

[alexweisberg]

Again, thank you very much for developing this tool, it has opened up several exciting new research projects for us.

It looks like Nanopore has just released beta models on rerio that now include 4mC modifications: https://github.com/nanoporetech/rerio (res_dna_r10.4.1_e8.2_400bps_sup@v4.3.0_4mC_5mC@v1).

I was wondering if MicrobeMod could eventually add support for these and report 4mC motifs as well?

Thanks!

[alexcritschristoph]

Yes, definitely! Will have a brief update that is imminent, and then this is next on the list.

[alexweisberg]

Great! Thank you. On Dec 11, 2023 at 6:50 AM -0800, Alex Crits-Christoph @.***>, wrote:

Yes, definitely! Will have a brief update that is imminent, and then this is next on the list. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[alexcritschristoph]

Included in https://github.com/cultivarium/MicrobeMod/pull/14 - let me know how it works for you! Seems to be working for me at the moment.

[alexweisberg]

Excellent thank you! I will try out both features. On Dec 31, 2023, at 11:56 AM, Alex Crits-Christoph @.***> wrote: Closed #13 as completed.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

[alexweisberg]

I tried it out and its working great for 4mC data. Thanks!

[Ge0rges]

How is 4mC annotated in output tables? The docs currently only show a and m

[galenptacek]

@Ge0rges modkit refers to 4mC by its ChEBI code (21839).

can refer to line 20 in microbemod.py: METHYLATION_TYPES = {"6mA": "a", "5mC": "m", "4mC": "21839", "5hmC": "h"}