SILVAngs -> biom.format -> data.visualization

Question

[tomaz-biostars]

Hi,

Being really good with computes, I just cannot find a way to transform a .csv result table from SILVAngs to a biom table that could be fed into any of the visualization software using the biom format.

I've been trying with R (biom, biom-utils), but cannot get it done. fax4fun - reads the .csv tables, but past the import...everything is a blur. megan6 - does not ready any of the silvangs .csv outputs ...

Is there a simple solution or are other options better? Any advice will be greatly appreciated! Thanks, Tomaž

Answer 1

[Tom]

Hi. Have you tried the biom conversion programs from biom-format project: http://biom-format.org/documentation/biom_conversion.html it might help.

Answer 2

[tomaz-biostars]

Hi. I understand that the SILVAngs .csv exported data is the problem. A regular data table (tab-delimited) can be transformed to biom without problems. Have not seen many people exporting SILVAngs data to be visualized elsewhere ... Cannot import any of their .csv files into Megan6 as well.