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!
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!
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.maier@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-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!
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" <xfwang@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.maier@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-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!
Hi Xiaofei, I just replied to the other thread about this same question, and left you on the cc. Please check out the cloud option - this is intended to be useful for those that do not want to invest in a local server or manage the associated administrative tasks. If you are working in on a project related to academic research, be aware the Amazon has a grant program that can help with the costs there (Galaxy is free of course!). More details about this are on their web site. http://usegalaxy.org/cloud http://aws.amazon.com/grants/ Good luck with your project! Jen Galaxy team On 2/14/14 9:39 AM, Wang, Xiaofei wrote:
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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participants (3)
-
Jennifer Jackson -
Wang, Xiaofei -
Wolfgang Maier