Dear Forum,
I have taxonomic assignment files (see below - is there an official name for this file format?) for each of my sequences and I have a file per sample. I would like to create summaries (abundance tables) and use these tables to create graphs (e.g. pie-charts and bar-plots or heat-maps to compare samples). Does anybody know (flexible) command line tools or R libraries that I could use?
Thanks for considering my question!
File format:
I have taxonomic assignment files (see below - is there an official name for this file format?) for each of my sequences and I have a file per sample. I would like to create summaries (abundance tables) and use these tables to create graphs (e.g. pie-charts and bar-plots or heat-maps to compare samples). Does anybody know (flexible) command line tools or R libraries that I could use?
Thanks for considering my question!
File format:
Code:
Seq1 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli Seq2 Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Staphylococcus;Staphylococcus epidermidis Seq3 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Rhodobacter;Rhodobacter sphaeroides;Rhodobacter sphaeroides 2.4.1 Seq3 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Rhodobacter;Rhodobacter sphaeroides Seq4 Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Staphylococcus;Staphylococcus epidermidis
