Using multiple depth files

[Former user]

Hello - I have looked around I can't seem to find an answer to my question. I have metagenomic data from six samples that are similar to each other, and I wanted to improve my binning for each sample using depth information from multiple samples. Is it possible to give the multiple depth text files separated by commas to the -a argument when running metabat2?

[Rob Egan]

no metabat only accepts a single abundance file. You can generate it from the full set of bam files, or write a simple script to append the new columns of the two abundance files.

BUT if you do not expect to see differential abundance profiles across the six samples, you might be better off combining them into a single abundance to get better signal on the lower abundance genomic species. YMMV, but metabat assumes that each sample adds new information that can be used to differentiate two genomes, not more of the same information.