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Old 02-26-2013, 05:48 PM   #7
seb567
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Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
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Quote:
Originally Posted by severin View Post
Sebastien,

This really is a nice tool. Sorry to bombard you with so many questions but I would like to know the limitations of the tools I am using.

Some of the runs I have experienced where not all the contigs are assigned to a species. In which case wouldn't this lead to a misrepresentation of what is present in the sample?
Do you mean that the percentage of unknown life forms is underrepresented ?

Quote:
Originally Posted by severin View Post

How hard would it be to also output the relationship between contig and Taxonomic level? ... Order family genus etc
It's just a matter of adding the code at the good place.

Quote:
Originally Posted by severin View Post

ie contig-001 Micrococcineae

In other cases every contig is assigned, in which case, how do we determine quality of match to a bacteria or virus if those are the genomes we are using when in actuality the contig belongs to a Eukaryote? Ie possible miss-assignment due to limited number of genomes in the search.
If you search for a virus, and a given mammal genome contains all the sequences
of the virus and this mammal genome is not provided to Ray Communities, then yes, Ray
will tell you that it's from a virus.

If you provide Ray Communities with the virus genome and the mammal genome, then the
software will look for those kmers that are not in common, if any.

Quote:
Originally Posted by severin View Post

Finally, How does kmer length affect ability to assign a contig to a species/taxonomic group?
Longer kmers are more specific.

Allowing mismatches would allow sensitive kmer search with large kmers. Mismatches
are not implemented at the moment.

Quote:
Originally Posted by severin View Post
Have you look at this?
Not a lot, honestly.

Quote:
Originally Posted by severin View Post

Thanks for all your help on this.

Regards,

Andrew
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