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Question: Megablast
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gravatar for Ali Tofigh
10.3 years ago by
Ali Tofigh • 10
Ali Tofigh • 10 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, /Ali
galaxy • 1.4k views
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modified 10.3 years ago by Anton Nekrutenko ♦ 1.7k • written 10.3 years ago by Ali Tofigh • 10
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gravatar for Anton Nekrutenko
10.3 years ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k wrote:
Dear Ali: 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: http://test.g2.bx.psu.edu 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. Thanks, anton galaxy team Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton@bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752
ADD COMMENT • link written 10.3 years ago by Anton Nekrutenko ♦ 1.7k
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