Importing Blast File Into Megan

Question

[vijay]

Hi All,

I am trying to work with MEGAN metagenomic analyzer to try try out some analysis on metagenomic data and I am a newbie to this field. I am getting stuck at the very first step of importing a blast file into Megan along with the file containing my reads. I am not sure on how to import a blast file into Megan.

Please can someone let me the step by step process of importing blast file into MEGAN?

I have read the manuals, but I am unable to follow the instructions clearly.

Your responses are highly appreciated.

-Vijay

Answer 1

[Istvan Albert]

To import a blast file simply select New then in the new window select Import From Blast file. Don't load the reads for now, those are needed only for certain special analyses, and if possible use a subset of your whole blast file so that you can work out the problems without having to wait for huge files to load in.

I will mention some of the problems I have ran into just in case. For Megan to work properly the sequences in the target databases (this is the database that you search for matches) need to be named in a way that corresponds to the taxonomical tree that the software has preloaded. Alternatively the sequence names need to be semicolon separated taxa names. What this means is that you either:

1. if you are using the NCBI nomenclature you will need to load a file listed under GI accession numbers to NCBI taxon ids
2. if you are using a custom nomenclature see the section titled How MEGAN Parses Taxon Names in the user manual.