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!
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:
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_highIs 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!