On 17/07/13 02:19 PM, Adrian Pelin wrote:
> I suspected it is enabled by default, since there is no mention on
> enabling it in the manual.
>
> Is there any info that Ray will produce, that could let me know
> something about the possible presence of multiple genomes? For example I
> know I have pseudomonas contamination, it would be nice if Ray could let
> me know the contigs of peudomonas that correspond to a specific kmer
> frequency based on the coverage of the contaminant?
Ray reports coverage values in
RayMicrobiomeAnalysis/
BiologicalAbundances/
_DenovoAssembly/
Contigs.tsv
*.CoverageData.xml <=============
see ray/Documentation/BiologicalAbundances.txt
>
> I also fear multiple strains in my sample, some info on that might be
> useful.
>
> Thank you.
> Adrian
>
> On 7/17/2013 10:05 AM, Sébastien Boisvert wrote:
>> On 17/07/13 01:02 AM, Adrian Pelin wrote:
>>> Hello,
>>>
>> Hi,
>>
>> Ray Meta mostly refers to the changes (generalizations) that were made pour
>> metagenomes.
>> These changes are there by default and are described in our paper [1].
>>
>> You are not the first person who is expecting an option to trigger the meta
>> part,
>> but the 2.x.y series have these changes enabled by default because they also
>> work
>> well on single genomes too.
>>
>>
>>
>> [1] http://genomebiology.com/2012/13/12/R122#sec3
>>
>>> Does anyone know how to start Ray Meta specifically? Do you need to pass
>>> certain args to the Ray process?
>>>
>>> I looked in the manual, and it say that Ray Meta is included in the
>>> package, but does it need to be triggered somehow?
>>>
>>> Thank you,
>>> Adrian
>>>
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