Thanks for Pavian, it's very useful. But, for us plant microbiologists, it could be better still!
In the summary table, the Microbial column is a catch-all consisting of all identified reads not classified as vertebrate or artificial etc. For shotgun plant metagenomes, that unfortunately includes all plant reads, so >95% of classified reads are "Microbial", of which variable proportions are plant vs actual microbes. I'd like to be able to add a column to the left of "Microbial" for p_Streptophyta (=Plants), and have these reads subtracted from the Microbial column.
I've hacked this together for my install by changing the data.table creation code for the summary table, and I would be happy to submit my change as a PR. However, it's likely that others would prefer to add their key eukaryotic organism(s) as non-microbial, so a better approach might be to ask the user for taxa (as strings like p_Streptophyta) for the "left hand" columns, and then keep the bacterial/protist/viral/misc microbial columns as they are now (but subtract all "left hand side" columns from Microbial, and perhaps rename it "other taxa").
Hello,
Thanks for Pavian, it's very useful. But, for us plant microbiologists, it could be better still!
In the summary table, the Microbial column is a catch-all consisting of all identified reads not classified as vertebrate or artificial etc. For shotgun plant metagenomes, that unfortunately includes all plant reads, so >95% of classified reads are "Microbial", of which variable proportions are plant vs actual microbes. I'd like to be able to add a column to the left of "Microbial" for
p_Streptophyta(=Plants), and have these reads subtracted from the Microbial column.I've hacked this together for my install by changing the data.table creation code for the summary table, and I would be happy to submit my change as a PR. However, it's likely that others would prefer to add their key eukaryotic organism(s) as non-microbial, so a better approach might be to ask the user for taxa (as strings like
p_Streptophyta) for the "left hand" columns, and then keep the bacterial/protist/viral/misc microbial columns as they are now (but subtract all "left hand side" columns from Microbial, and perhaps rename it "other taxa").Best, Kevin