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Old 02-20-2013, 01:06 PM   #2
severin
Genome Informatics Facility
 
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default Ray Meta

How do I include genomes other than the bacteria that are found in the NCBI-taxonomy directory that your script generates? I could drop the fasta file into a folder however...

Is there an easy way to include the taxonomy information about the genomes I add? You added Human in the paper, but if I wanted to include multiple species that the taxonomy is known do I have to do this manually or is there a tool that can help me achieve this?

Also, I am interested in not just obtaining the abundances but also assigning the scaffolds to particular species or other level in the taxonomy. Does Ray output the scaffold to taxon information somewhere?

One last question.
If I have an assembly from say Trinity can I run the assembly through Ray-Meta and have it return abundances based on the transcripts themselves? How dependent is the algorithm to have done the assembly prior? Can I feed Ray-Meta a kmer graph?


Thanks and really excited to use this tool.

Last edited by severin; 02-20-2013 at 01:08 PM.
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