Question: SnpEff fails to add expected annotation when run at http://usegalaxy.org
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gravatar for valeria.caro
22 months ago by
valeria.caro0 wrote:

what is the meanning of none in the table of Number of effects by type and region, thank you very much

ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by valeria.caro0

Which tool are you using?

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson25k

hello jennifer, I am using the SnpEff: Variant analysis tool, in the part of Number of effects by type and region

ADD REPLYlink written 22 months ago by valeria.caro0
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

My guess is that the data is not from the human reference genome hg19. That is the only human genome indexed for the tool at http://usegalaxy.org. There could be other factors - the inputs are all not from hg19, other content issues. Check for these.

If using Galaxy somewhere else, then the reference annotation for genomes you wish to use will need to be installed. Instructions are in the Tool Shed for this repository. If another public server, request this from those admins of the instance.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k

I am using the hg19 from 1000 genomes, I don't know why this is happening, also I want to now what is the meanning of "motif" in the same table, thank you very much

El 21 oct. 2016 1:47 PM, "Jennifer Hillman Jackson on Galaxy Biostar" < notifications@biostars.org> escribió:

ADD REPLYlink written 22 months ago by valeria.caro0
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