Basic Process Flow For Metagenomic Analysis With Megan V 4.Xx

Question

[Dhruv Sakalley]

I am trying to run and test MEGAN for any given project, lets say role of human gut microbiota for ulcerative cloitis. Here is the project link http://www.ncbi.nlm.nih.gov/genomeprj/46881 I am finding it hard to download and format data as required for MEGAN Analysis. Does anyone know the steps required for data acquisition for metagenomics (When you are not doing the experiment, just using the available data posted by someone).

I would like to know how to get to the Filename.blast from original raw data which MEGAN uses

Answer 1

[Istvan Albert]

Groups typically post original reads as produced by the instrument. You can access those via the Project Data --> SRA link.

Now Megan uses as input the output of running blast on those reads. This file was most certainly not generated unless the project actually needed that type of analysis. Moreover even if this file was created originally it will most likely not be available from NCBI.

You may want to ask the original authors or alternatively run the blast process yourself. Note that it will be extremely computationally intensive!