Problems Using Aachanges Tool

Question: Problems Using Aachanges Tool

7.8 years ago by

Evan Schwab • 60 wrote:

Hi, I am trying to use the aaChanges tool. I have a file of SNPs in the correct interval format and a UCSC uploaded bed file of genomic intervals. These are both for the Zebrafish Zv9 build and are appropriately labeled this way in their attributes. But when I try to run the tool it says for both the SNP interval file and UCSC bed file: "Sequences are not currently available for the specified build." Am I doing something wrong with my formatting or does this tool not yet support Zebrafish Zv9 build? I tried using it in the Human Genome Variation section of the main Galaxy site as well as the Evolution section of the test site and both gave me the same error. Please let me know what is happening. Thank you so much Evan -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

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modified 7.6 years ago • written 7.8 years ago by Evan Schwab • 60

7.8 years ago by

Evan Schwab • 60

Evan Schwab • 60 wrote:

ADD COMMENT • link written 7.8 years ago by Evan Schwab • 60

7.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Evan, Would you be able to share a link to your history and we can take a look at exactly the problem data/tools. Use Option -> Share or Publish. Best! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

7.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Vasu, Are you still have problems? Updating to the most current distribution dated Feb 18th would be advised, as a starting point: hg pull -u -r ca0c4ad2bb39 https://bitbucket.org/galaxy/galaxy- central/wiki/Features/DevNewsBriefs Please give this a go and let us know if there continue to be issues with using the save icon on your local instance. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

7.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Evan, The update to include zebrafish (and a few other genomes) should roll out to Galaxy main in the next few days, if not sooner. Feel free to check back Friday for an update if you do not see it there by then. Thank you for your patience! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

7.6 years ago by

Evan Schwab • 60

Evan Schwab • 60 wrote:

Hi Jen, I am still having troubles with the aaChanges tool because it doesn't support the Zebrafish Zv9 build. But then as a test I annotated my data as Zv8 as well as the mm9 genome builds and the same error occurred. Is it a problem with the tool itself then and not my specific build? Thanks Evan -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

ADD COMMENT • link written 7.6 years ago by Evan Schwab • 60

Jen, I am still seeing no change with the aaChanges tool. This tool is very important to my analyses at the moment. Can you please give me an update on the fixing of this tool. Thanks Evan On Wed, Apr 13, 2011 at 10:49 AM, Evan Schwab -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

ADD REPLY • link written 7.6 years ago by Evan Schwab • 60

Hi Evan, There is some work being done for a permanent link to the dataset, but it is still pending. So, we are going to attempt a short term solution and I will send you an email once I confirm it is in place. I don't know exactly when this will be ready - but the goal is for it to be soon. Thank you again for your patience! Jen -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k

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