Mg-rast --> megan

ewilbanks · 03-10-2013, 12:39 PM

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!

rhinoceros · 04-14-2013, 05:45 AM

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?

rhinoceros · 04-16-2013, 08:35 AM

Great news! I was wrong. It's possible. Have a look here.

SDPA_Pet · 09-07-2013, 02:38 AM

Quote:

Originally Posted by rhinoceros

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

rhinoceros · 09-08-2013, 10:21 PM

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)..

SSyeda · 12-06-2014, 04:08 PM

Hi,
Have you had any luck in figuring out using data from MG-RAST into MEGAN?

Thanks.

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03-10-2013, 12:39 PM	#1
ewilbanks Member Location: Davis, CA Join Date: Mar 2009 Posts: 82	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!

04-14-2013, 05:45 AM	#2
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	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 06:08 AM.

09-08-2013, 10:21 PM	#5
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	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 10:30 PM.

04-16-2013, 08:35 AM	#3
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	Great news! I was wrong. It's possible. Have a look here.

12-06-2014, 04:08 PM	#6
SSyeda Junior Member Location: Illinois Join Date: Dec 2014 Posts: 1	Hi, Have you had any luck in figuring out using data from MG-RAST into MEGAN? Thanks.