I’m new to MEGAN (and loving it!) and I’m using it for 16S rRNA data after processing it in mothur. My OTU table is subsampled, i.e. all samples contain 14,000 reads. However the linear Stacked Bar Chart shows different total number of reads for each sample, some as low as ~2,000. What does this mean? Does MEGAN exclude OTUs with abundance below a certain cutoff value? If yes, what is that cutoff?
What scale do you recommend, then, for comparing relative OTU abundances across samples: linear, (provided that all samples have the same number of reads), square root, log or percentage?
The chart viewer shows numbers for whatever is selected in the main viewer, is that causing the discrepancy?
I would normalize the samples and then use a linear scale.
Hi Daniel, many thanks for your reply - I’ve only just seen it. I don’t think I’ve selected anything in particular in the main viewer, i.e., I’d expect to see all OTUs in the chart viewer. The OTU table had already been normalised to 14,000 reads per sample prior to making a biom table and importing it to MEGAN. Yet in the linear scale of the stacked bar plots I see varying total number of reads for each sample instead of 14,000 for each sample. Are singleton OTUs excluded from the chart or something like that?
I look forward to your reply!
Many thanks for your time,
Julia
If you don’t explicitly select anything in the tree viewer, then MEGAN will select all leaves for you (except the no hits and unassigned nodes). If you want everything to appear, then you need to explicitly select ALL nodes.