Number of marker genes per species.

[ailtonpcf]

Dear developers,

Thank you for this really cool tool. I am using another tool to profile eukaryotes and there I know how many marker genes were detected per species. This is also important for normalization because the raw counts increases with the number of markers. I've read the thread #108 and I was wondering if it's already implemented somewhere in the tool. I mean, is there a way to know how many markers were detected per species?

Bests,
Ailton.

[hjruscheweyh]

Dear @ailtonpcf
Thank you for your interest in mOTUs. There are multiple questions in your thread. I will answer as bullet points:

1. mOTUs is operating on universal single-copy marker genes which means that a length normalisation is not needed between species (mOTUs) (https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.218, Figure 3). This means that you dont need to normalise by the number of genes with abundance.
2. If 1. doesnt work for your analysis - You can run mOTUs with reporting the marker-gene-cluster abundances (-M) which will report the abundances of all marker-gene-clusters. E.g. A mOTU consists (in the best case) of 10 marker-gene-clusters, one for each of the 10 marker-genes.

Hope that helps. Lets me know if more feedback is needed.

Hans