Thank you so much for your reply! But, may I double check what do you mean by 
"try the Mapping tool individually"?

"maybe try the Mapping tool individually first with some test data to see 
whether you are getting any result at all."

You mean I should try the tools individually (like BWA for map, GATK for 
calling SNPs, ...) by hand not use the CloudMap pipeline on Drosophila?

Thanks
________________________________
From: Wolfgang Maier [wolfgang.ma...@biologie.uni-freiburg.de]
Sent: Friday, February 14, 2014 11:48 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm 
(galaxy not local)

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-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@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!
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