Get taxa information from MEGAN

[SDPA_Pet]

Hello, I am using MEGAN (http://ab.inf.uni-tuebingen.de/software/megan5/) to analyze my metagenomic data.
I am using MEGAN 4.X to analyze my metagenomic data. I was wondering if there are any faster ways to extract all taxonomic information from some KEGG functions that I am interested in. After I load my data (BLAST results) in MEGAN, I click KEGG button. Then, I can find a function group that I am interested in. Let's say I am interested in Energy Metabolism --> Sulfur Metabolism. I find I have 200 reads assign to E.C. 2.5.1.47 (Also assigned to K10150, K12339, K01738). After I click inspect, it give me which taxa are assigned to K10150, K12339, K01738. For each KEGG function, there are several reads assign to the function and you can see the bit scores, e-values and taxonomic names. I would like to find the best taxa (i.e. most closest, high bit scores) assigned to each function. Now, I have to go over one by one manually and record the bit scores by hand, until I find the highest.
Is there any fast approach to extract the taxa assigned to certain KO functions to a table? For example, I want to get the taxa name that assign to function K10150. So, I can sort it by bit scores and won’t miss any taxa.

I read lots of paper. They use MEGAN and find the functions that the authors interested in. Also, they give the the taxa assigned to those functions. I'm not sure how they did it.

Thanks,
Ben

[Polecat]

Did anyone have an answer for this as I have the same question? I am doing soil metatranscriptomics and in MEGAN 5 I have a particular KEGG ID I am interested in and want to see the taxa of the organisms that this KEGG sequence is in.

Does anyone know if you can extract this information from KEGG, SEED or COG ids of interest?

[Polecat]

I think from RTM that what I need to do it go to File -> Export Alignment to get this info but I can't do this as I get a java.io.IOException error. Anyone know if this is due to my supercomputer cluster or is it a MEGAN error?

TIA.

[bashma]

I Think the easiest way to do so is to use the export function. Go to the TaxViewer --> uncollapse all --> select all leaves --> export read name - taxon path.

Then switch to KEGG COG or SeedViewer.
again --> uncollapse all --> select all leaves --> export read name - kegg path.

afterwards you can combine these files to find out which read/scaffold was classified as what.

cheers,
Mina

[Polecat]

here in lies the problem. When I try to do exactly what you have listed about Mina for the COG viewer the Export -> Reads tab is greyed out and I can't hit it. Only the export csv, biome, metadata and coverage vs GC content are available.

doing the export csv only tells me COG Id, path and and abundance. There is no info on reads there

The same thing happens from the taxonomy side, the reads button is greyed out.

[Polecat]

I did find out that I can export from the individual .rma files for each of my samples for a select COG or taxa. The export function for some stuff appears to be unavailable when you're working with comparisons of multiple samples in a .megan file.