Hello,
I have a dataset of shotgun sequences, and I am interested in using the diversity measurements of mothur to analyze my samples. I have generated contigs, and calculated average base-pair coverage for each contig. This helps to normalize the differences in contig length. I am wondering if I can use this data file, containing coverage of contig per sample as a “shared” file, and input it into the dist.shared and downstream commands. In this case, the [contig coverage = # sequences per sample] and [contig number = OTU]. I am trying to determine how mothur computes distances for non-interger values (in my case, contig coverage is often a decimal). An alternative would be to multiply all of my coverages by a fixed value so as to get all interger values.
Thank you in advance for any help!