Hi, I am completely new to MEGAN and I would like to import some SILVA results data to MEGAN for comparison studies. What I want to do is to classify my sequences against SILVA database and import the results into MEGA with corresponding SILVA taxonomy. In MEGAN manual I found the following information:
“Similarly, MEGAN can import rRNA analysis files downloaded from the Silva website at http://www.
arb-silva.de [20]. To create a file using the Silva website that can be imported into MEGAN, go to
the Aligner tab of the Silva website and upload your sequences and then press the align sequences button. Once the Silva website has computed an alignment, you will be able to download two files, an arb file and a log file. MEGAN requires the log file as input, not the arb file. When importing such a file into MEGAN, one must specify that MEGAN uses the synonyms file called silva2ncbi.map to map Silva accession numbers to NCBI taxa. This file is available from the MEGAN download page.”
that I am unable to follow. On SILVA aligner page I uploaded my MULTI FASTA file and checked options “search and classify”, “compute tree” and “ARB”. After running the program I downloaded the resulting arb and log file. The log file I tried to import to MEGAN, but I filed, as MEGAN states it cannot recognize the input format and mode. I am also not sure which file should I pass to MEGAN as synonyms file as the silva2ncbi.map file stated in the manual is not available fromMEGAN download page (at least I do not see it there). I have used, hopefully correctly, SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map instead. I forced MEGAN to open by selecting BlastText (I know it is not correct) as format and BlastN as mode, but I could see only the default all kingdom cladogram there.
I would be very grateful for any advice on the topic, as I am unable to find any hints in other discussions.
Thanks,
Hana