Synonym File

Question

[fanx]

I am using MEGAN4 to parse SAM file generated by Bowtie, i.e., 454 read mapping against NIH virus reference database. MEGAN4 requires a corresponding synonyms file. Does anyone know how to create this synonyms file from NIH reference database? Thanks. fanx

Answer 1

[Alex Paciorkowski]

I assume you checked here (.pdf) and here (MEGAN3.9 unfortunately) already -- and it seems the synonyms files are custom files, perhaps are locally generated? The syntax is described in the documents I reference, but there doesn't seem to be a source to download a sample from. I would email the authors of the tool, or see if any of your colleagues working with the same tools have an example they might share.