I meant you should try just the EMS Variant Density Mapping
tool with a small sample vcf file from Drosophila because
the problem if it still exists will occur at this last
step.
Best,
Wolfgang 


On Fri, 14 Feb 2014 18:42:28 +0000
 "Wang, Xiaofei" <xfw...@ku.edu> wrote:
> 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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