How to export reads of Chart Microbial Attributes result?

User Questions
1

Dear MEGAN community,

I found something interesting of the Chart Microbial Attributes results, and I’d like to export the aligned reads of some categories of it (e.g. Disease) for further verification. For example, there is 500 reads assigned to Disease: Glanders and Pneumonia, and how can I know the sequence of these 500 reads?

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And another question is how Megan perform the microbial attributes? In the manual it says “The classication and its nomenclature is based on the NCBI’s
prokaryotic attribute table (derived from: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi )”, but there is no details of it. I checked the website and I didnot find the “Disease” category.

Thank you for your nice tool.

Chen

1 Like
2

Dear Chen,

this is a very old feature of MEGAN that was based on a file that NCBI used to provide (until 2012), but don’t provide anymore. Here is the file that megan uses: microbialattributes.map (1.1 MB)

From this file, you can figure out which taxa map to Disease:Glanders and Pneumonia.
Put those in a file, one per line and then use the Find “from file” feature of MEGAN to select all nodes in the taxonomic view of your data, then use the extract reads features to extract all reads matching those taxa to a file.

Hope that helps
daniel

1 Like
3

It works! Thank you Daniel!!

Best,

Chen