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Old 03-10-2013, 01:39 PM   #1
ewilbanks
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Default Mg-rast --> megan

Does anyone if it's possible to grab output from MG-RAST and feed it into MEGAN? The all vs. all BLAST search required for my dataset would be hideous on our servers and I was hoping to use something MG-RAST generates. I have some downstream analysis better done in MEGAN and essentially just want to use MG-RAST for its annotation and BLAST searches.

Ideas anyone?

Thanks!
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Old 04-14-2013, 06:45 AM   #2
rhinoceros
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I think MEGAN requires NCBI GIs for the hits. However, as far as I can tell, MG-RAST (also IMG/M) does not assign these. Perhaps you could extract subsets of interest from MG-RAST results and blast those against NCBI's nr?

Last edited by rhinoceros; 04-14-2013 at 07:08 AM.
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Old 04-16-2013, 09:35 AM   #3
rhinoceros
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Great news! I was wrong. It's possible. Have a look here.
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Old 09-07-2013, 03:38 AM   #4
SDPA_Pet
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Quote:
Originally Posted by rhinoceros View Post
Great news! I was wrong. It's possible. Have a look here.
Hi rhinoceros,

Have you ever done this? From MG-RAST to MEGAN. I tried, but I couldn't export the NCBI annotation format from MG-RAST.

If you did it successfully, can you tell us the details?

Thank you
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Old 09-08-2013, 11:21 PM   #5
rhinoceros
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Hey,

No, I haven't done it. However, it shouldn't be so hard. Go to the download page of the genome you're interested in and check under "Annotation Download via API". From this you get tab-delimited files that could perhaps be imported into mg-rast like normal tabular blast output. If that doesn't work, then you need to apply some cut and paste at the command line (probably replace the second column with the last column)..

Last edited by rhinoceros; 09-08-2013 at 11:30 PM.
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Old 12-06-2014, 05:08 PM   #6
SSyeda
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Hi,
Have you had any luck in figuring out using data from MG-RAST into MEGAN?

Thanks.
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