Normalization on Pfam Analysis

User Questions
1

Hi there!

I’m working with 6 metagenomic samples with very uneven number of reads - I’m trying to analyze both taxonomic and functional contents of these samples. When using the “Compare” function, the “Use normalized counts” option works fine for Taxonomy analysis (based on in-built NCBI taxonomic classification) but it isn’t able normalize the number of reads associated with Pfam IDs.

Is MEGAN able to use normalized counts on functional analyses (specifically Pfam families), or is this option only available for taxonomy assignments? If it’s possible, I’d be very thankful if you could give me instructions on how to do this kind of analysis, since I’m clearly making something wrong.

Thanks in advance for your suport!

Kind regards,
Cândice.

2

At present MEGAN normalizes with respect to the number of taxonomically assigned reads. Functional classifications are also normalized, but with respect to the number of taxonomically assigned reads. However, what you suggest, namely normalizing each classification separately by its own number of assigned reads, is perhaps a better way to do things and I will look into implementing it.

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