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Old 06-02-2015, 10:30 AM   #1
Location: Argentina

Join Date: Feb 2013
Posts: 19
Default MG-RAST - Efficient downloads?

I want to download the hierarchical SEED Subsystems information for 30 metagenomes at MG-RAST. I've managed to obtain, through the API, the tables corresponding to the 4 levels separately, but I'd like to have the integrated table you obtain from the "Analysis" section. In this table you can actually see the hierarchy of this system.
The thing is that when you ask MG-RAST to include so many samples (30), it kind of crushes.
Does anyone know a better way? Maybe via the same API?
fibar is offline   Reply With Quote
Old 06-26-2015, 05:03 AM   #2
Location: CANADA

Join Date: Nov 2013
Posts: 24

Please before download the SEED subsystems check the validity of MG-RAST annotations. I was surprised that there is a lot of crushes and errors in annotations. Please compare the orfs.faa or orfs.fna to the SEED organisms or functions annotations, we will find not corresponding data for example the start-end of orfs in query is different then start-end of query gathered in annotations files. I have started to suspect the quality of MG-RAST annotations. Every biologist should not believe in black box of automated things software and webservers might suggest control test for each step in data processing.
Bachbioinfo is offline   Reply With Quote

comparison, download, metagenomics, mg-rast

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