Exporting prokaryotic reads


Is there an option to export only subsets from the functional annotations, based on selections from the taxonomic tree?

I am trying to export SEED subsystems that match only bacteria


The (only) way to do that at present is to use the “Extract to new Document” feature:
First, select all the Bacterial nodes and use “Extract to new Document” to make a new document that only contains those reads that have been assigned to a bacterial node.
Then, use the new document to export the functional annotations of interest.

Hi Daniel:

I found this question as it covers exactly what I would like to do, but somehow bacterial species numbers doesn’t match at all when comparing the original diamond alignment file and the extracted document. For example, on the extracted file I can only see 6 bacterial species while in the original diamond file there are at least 40 bacterial species.

What I did was to select the Bacteria node, then select the whole subtree and then use “Extract to new document”. This on Megan 6.8.12.

What could I do? what I’d like to do is to grab everything bacteria-related and then perform SEED/COG analysis.



I’m not sure what is going on there, but it might be related to the fact that after extraction, the LCA taxonomic binning algorithm is rerun on the extracted set of reads and this may lead to classification differences. Please check whether this is the case, otherwise, please let me see more details.