Re: [Denovoassembler-users] Question about Ray Meta?

[Sébastien B. <se...@bo...>]

To understand the differences, go read the paragram "From Ray to Ray Meta"


http://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-12-r122#Sec11


________________________________
From: Vishal N Koparde <vnk...@vc...>
Sent: June 22, 2016 5:28 AM
To: Sébastien Boisvert
Subject: Re: Question about Ray Meta?

So it auto detects if the input reads are coming from one genome versus a metagenome??

Vishal Koparde, PhD
Bioinformatics Scientist
Virginia Commonwealth University
Richmond VA USA




On Wed, Jun 22, 2016 at 7:27 AM -0400, "Sébastien Boisvert" <se...@bo...<mailto:se...@bo...>> wrote:


There are no difference. There is a section in the Genome Biology 2012 explaning the changes made to the software.

________________________________
From: Vishal N Koparde <vnk...@vc...>
Sent: June 22, 2016 5:21 AM
To: Sébastien Boisvert
Subject: Re: Question about Ray Meta?

I understand that part. Could you please point out the difference in commands if I am assembly a single genome versus a metagenomic assembly??

Vishal Koparde, PhD
Bioinformatics Scientist
Virginia Commonwealth University
Richmond VA USA




On Wed, Jun 22, 2016 at 7:19 AM -0400, "Sébastien Boisvert" <se...@bo...<mailto:se...@bo...>> wrote:


Ray Meta is the collective name for the set of option to perform profiling in Ray.


________________________________
From: Vishal N Koparde <vnk...@vc...>
Sent: June 14, 2016 8:13 PM
To: Sébastien Boisvert
Subject: Re: Question about Ray Meta?

I have submitted the question on github too. But, since i didn't get any response, I thought I would email you directly.

Vishal Koparde, PhD
Bioinformatics Scientist
Virginia Commonwealth University
Richmond VA USA




On Tue, Jun 14, 2016 at 10:12 PM -0400, "Sébastien Boisvert" <se...@bo...<mailto:se...@bo...>> wrote:


Please send your questions to the mailing list. I will answer to the mailing list.


________________________________
From: Vishal N Koparde <vnk...@vc...>
Sent: June 3, 2016 8:26 AM
To: se...@bo...
Subject: Question about Ray Meta?

Hello Seb,
I have successfully compiled and run Ray, but have no clue how to run Ray Meta? What is the difference in the command line to run Ray Meta vs. Ray vanilla? I have a metagenomic sample with 3 closely related species as a test case.
Thanks,
-Vishal

Vishal N Koparde, Ph. D.
NGS Bioinformatics Scientist,
Nucleic Acid Research Facilities/
Center for Study of Biological Complexity,
1101 East Marshall Street, #5-050,
P.O. Box 980678
Virginia Commonwealth University
Richmond VA 23298-0678
Email: vnk...@vc...<mailto:vnk...@vc...>
Phone: +1-804-628-3060