Determine Sample with Enriched Modification

max-vdL commented 11 months ago

Hi, I’m currently working with the Master of Pores 2 to detect RNA modifications. In my analysis, I need to determine which of the two samples being compared has an enrichment of modified RNA at position X.

However, in the final output, I only receive information about differences at the supported k-mer positions. In epinano does indicate the enrichment trend toward a specific sample, but I haven’t found such an indication in nanoconsensus or nanoposish/compore.

Have you encountered this issue before or found a way to extract sample specific enrichment information?

lucacozzuto commented 8 months ago

@ADelgadoT

ADelgadoT commented 7 months ago

Hi Max,

As you mention, NanoConsensus and Nanocompore only give qualitative information (ie: which regions are differentially modified between samples) and they do not give information regarding the directionality of the change.

To obtain this information, you should either:

Option 1 (recommended): look at epinano summed errors
Option 2: check the results of tombo msc - they contain information about % methylated reads per position - and therefore, it could give you an idea of the directionality.

Thanks a lot!

biocorecrg / MOP2

Determine Sample with Enriched Modification #53