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Question: Getting species/taxa from GIs
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gravatar for neptune24
23 months ago by
neptune24 • 10
United Kingdom
neptune24 • 10 wrote:

Hi there, I'm using megablast to find out whether my RNAseq data might contain contamination from other genomes. How can I convert my list of Geninfo Identifiers from the nt or htgs databases into taxa and gene names? I've looked some of them up individually but would like to find a tool in usegalaxy or elsewhere online (similar to DAVID) that could convert the whole list if possible.

Many thanks
gi blast • 591 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 23 months ago by neptune24 • 10
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool DAVID is included at the public Galaxy Main server http://usegalaxy.org and is in the Tool shed http://usegalaxy.org/toolshed (from where it can be installed into a local/cloud Galaxy). At Galaxy Main, it is organized under the tool group Phenotype Association.

Other metagenomic tools do this type of association are in the tool group Metagenomic Analysis. These require a different type of input. I wanted to mention that in case you haven't settled on a method or want to compare methods.

The tool that previously derived this information from Megablast output is no longer supported at Galaxy Main, but it is in the Tool Shed (here). Be aware that the set up will take some time due to the size of reference files used, and that you might need to remap against the same version of ht/htgs as NCBI is currently publishing taxonomy data for.

Hopefully one of these options works out for you, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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