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
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
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