Question regarding region-based DMR analysis

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
48/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Active
Tech stack
rust
Domain
bioinformatics, cli

Research direction

Start with the modkit dmr pair command and the supplied target-region workflow described in the issue. Review how the reported BED fields are produced, then determine whether site counts and a minimum-site filter can be exposed; done means users can identify or restrict regions with at least three sites and the behavior is documented or tested.

Written by the indexing model from the issue text.

Description

Hi,

Thank you for developing a fantastic tool. I had a question regarding DMR analysis with supplied target regions. We have performed a sliding-window like analysis on our datasets which worked, but we need to know the number of unmod/modified sites within these small regions contributing to the call of 'differentially modified region'. We are, for instance, more interested in regions containing at least 3 sites versus those with a single site. Our end goal is to find small (~200 bp) regions with 3 or greater sites that are differentially modified between two conditions. We have done this using replicates (3 for each condition).

This is the current approach:

    modkit dmr pair \
        --ref ${ref} \
        -r ${regions_bed} \
        ${aArgs} \
        ${bArgs} \
        --base ${mod.base} \
        --single-code ${mod.code} \
        --threads ${task.cpus} \
	--header \
        --log-filepath ${comp_name}_${mod.name}.log \
        -o ${comp_name}_${mod.name}_dmr.bed

The resulting header is:
chrom start end name score strand a_counts a_total b_counts b_total a_mod_percentages b_mod_percentages a_pct_modified b_pct_modified effect_size cohen_h cohen_h_low cohen_h_high

Is there a way to know the number of sites within DMR's of interest? Or perhaps to force the analysis to report only those with >3 sites? Advice on the best way forward to achieve this would be great.

Many thanks!

Dominant language
Rust
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Forks
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