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Old 03-31-2015, 08:41 AM   #1
salamay
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Default sam2rma Tool in MEGAN

Has anyone been able to use the sam2rma standalone tool provided with MEGAN? I can't seem to get it to perform taxonomic classification, although I can get functional classification through KEGG, SEED, and COG to work. Taxonomic classification seems to be set to true by default, and there is no indication that I need to specify a taxonomy mapping file as I believe it is provided by default, but all my queries are labelled as "not assigned". Any help would be appreciated!

Thanks.
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Old 03-31-2015, 09:40 AM   #2
yzzhang
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Actually, if you import sam file, you also need to specify taxonomy file from MEGAN wedsite to get the taxonomy information. As the description "If the BLAST or other comparison files do not contain taxon names, but do contain GI numbers, then load the following mapping file to allow MEGAN to determine taxon names. The file has to be unzipped before it can be used:
http://www-ab.informatik.uni-tuebing...March2015X.zip
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Old 04-01-2015, 07:18 AM   #3
salamay
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Quote:
Originally Posted by yzzhang View Post
Actually, if you import sam file, you also need to specify taxonomy file from MEGAN wedsite to get the taxonomy information. As the description "If the BLAST or other comparison files do not contain taxon names, but do contain GI numbers, then load the following mapping file to allow MEGAN to determine taxon names. The file has to be unzipped before it can be used:
http://www-ab.informatik.uni-tuebing...March2015X.zip
Thank you very much yzzhang, that worked perfectly. I was incorrectly assuming that a gi to taxon file was provided by default. Thanks again.
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