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MicrobialDarkMatter / nanomotif

Nanomotif - a tool for identifying methylated motifs in metagenomic samples
MIT License
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Question: Read vs contig level analysis #35

Open nschuiling opened 2 months ago

nschuiling commented 2 months ago

In my analysis I am interested in obtaining (1) methylation motifs, (2) (non)methylated occurrences of those motifs at the read level. The output of nanomotif seems highly relevant for this, but is at the contig rather than read level.

I was therefore wondering whether it would be possible to provide binned reads (instead of contigs) as input: a .fasta reads file and a read-to-bin .tsv. How/Would this affect the results?

SorenHeidelbach commented 2 months ago

It is not something that is possible to do with Nanomotif. But, it is something we might look into in the future. To achieve it now, you would have to create a pileup formatted file of the certainty of methylation at each position of the read.

Best regards Søren