dist.shared with shotgun data


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!


You would need to convert the data into integers. Perhaps multiple by 10 or 100 and then round?