Last time I checked the EMS Variant Density Mapping tool, specifically, had an unnecessary restriction to chromosome names as in WS220.64 (chrI, chrII, chrIII, chrIV, chrV, chrX). So maybe before putting too much effort into the SnpEff side of the workflow, maybe try the Mapping tool individually first with some test data to see whether you are getting any result at all.

Best,

Wolfgang

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Wang, Xiaofei
Sent: Friday, February 14, 2014 6:40 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)

Dear,

Is it possible to use SnpEff with genomes of other species (e.g. Drosophila) other than C.elegan on galaxy website (not local)? It seems the only option for the genome menu (Caenorhabditis elegants : WS220.64).

In fact, I am trying to use CloudMap (the EMS Variant Density Mapping workflow) to analyze data for Drosophila. So, I have to edit the workflow based on my own data. For SnpEff on the workflow, I tried to change "Genome" to other species from Caenorhabditis elegants : WS. But, there is no other options. Then, I changed it "to be set at runtime". When I run the workflow, I still can not change it to other species. Then, I went to see the SnpEff tool on galaxy website and found that there is no other options for "Genome" option.

So, could you help me about this? Could I use SnpEff and CloudMap (the EMS Variant Density Mapping workflow) other than worm? Or, I have to install galaxy locally for this objective?

Thank you so much!

Have a nice day!