The megablast tool in the current version of Galaxy is adopted for
running metagenomics-type searches against nt (non-redundant
nucleotide) and wgs (whole genome short gun reads) databases. If you
would like to compare a series of reads against human genome, use
blat which is available at the test-site:
However, running whole genome mapping jobs is a substantial talk and
may take a while to complete. We are in the process of designing
short read analysis pipelines and all related tools are in
preliminary stages of development. In fact, Blat is not ideal for
mapping (it will do ok with longer 454 reads) and will have other
specially designed tools for this in the very near future.
On Aug 18, 2008, at 1:52 PM, Ali Tofigh wrote:
I have a large set of short reads (from human) that I'm trying to
analyze with galaxy. Specifically I want to map my nucleotide
sequences to the human genome. I found the "short read analysis"
section of galaxy. However, I can't seem to find any information on
how to interpret the output from megablast. Could someone tell me
what the numbers in the different columns represent?
And when chosing target databases, what is "nt" and "wgs"?
Thanks in advance,
galaxy-user mailing list
Department of Biochemistry and Molecular Biology
Center for Comparative Genomics and Bioinformatics
Penn State University