Determining the abundance of bins

[mradz19]

How do I go about determining the abundance if bins within samples? I've seen online that some programs calculate this but from what I can see in the bin table it only gives you coverage and TPM stats for the bins per sample.

[fpusan]

You can do this within SQMtools. Once you load your project as a SQM project, you can find different matrices within SQM$bins. E.g. SQM$bins$percent will contain the percentage of reads assigned to each bin in each sample. I personally like to use cpm (coverage per million reads) to track the abundance of bins. We also have a plotBins function, similar to plotTaxonomy, to quickly make barplots with the abundance of the most abundant bins in each sample.