Question: How to add Triticum aestivum snpEff4.3 genome database or appropriate wheat genome database in Galaxy for VCF annotation?
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gravatar for pltbiotech_tkarthi
8 months ago by
CIMMYT, Mexico
pltbiotech_tkarthi170 wrote:

I added the T. aestivum snpEff4.3 genome database in Galaxy (https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2FsnpEff%2F4.3%2BT.galaxy1&version=4.3%2BT.galaxy1&__identifer=rjgm18erx4), seems the database has been added as I could see theT. aestivum snpEff4.3 genome database at the right side history of Galaxy page column. But, when I add VCF file and snpEff4.3 wheat database, it's showing error. I would like to annotate the natural variants against the wheat genome (particularly against wheat homeolog 3DL). I also tried with VEP ENSEMBL, it is working, but I would like to try with Galaxy to see the annotations from Galaxy. Does anyone know about this?

genome • 283 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by pltbiotech_tkarthi170

You should post this question over at Galaxy help site.

ADD REPLYlink written 8 months ago by genomax73k
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