Dear Galaxy staff,
I have recently started using your tool and it has been really helpful, thank you! When using Human Genome Variation, aaChanges, I would like to keep some extra lines in the output file from either of the input files. In the tool description it says I should be able to keep them:
"...chromosome, start, and end position as well as the SNP. The SNP can be given using ambiguous-nucleotide symbols or a list of two to four alleles separated by '/'. *Any other columns in the first input file will not be used but will be kept for the output*. The second input file contains..."
However, I haven't found a way of actually have them in the output file. What am I missing/doing incorrectly? What I've been trying to keep by the way is rs IDs or Ensembl gene IDs.
Thank you in advance for your answer. Kind regards,
Ximena
Hello Ximena,
Thank you for bring this to our attention, we are able to duplicate these same results. A "name" attribute (such as an rs number) is an important data tag and we would like to be able to have the tool retain this data if possible. Our development team is currently investigating and we will get back to you as soon as possible.
Again, we appreciate your feedback and thank you for your patience while we review potential remedies,
Best,
Jen Galaxy team
On 5/25/11 5:22 AM, Ximena Bonilla wrote:
Dear Galaxy staff, I have recently started using your tool and it has been really helpful, thank you! When using Human Genome Variation, aaChanges, I would like to keep some extra lines in the output file from either of the input files. In the tool description it says I should be able to keep them: "...chromosome, start, and end position as well as the SNP. The SNP can be given using ambiguous-nucleotide symbols or a list of two to four alleles separated by '/'. *Any other columns in the first input file will not be used but will be kept for the output*. The second input file contains..." However, I haven't found a way of actually have them in the output file. What am I missing/doing incorrectly? What I've been trying to keep by the way is rs IDs or Ensembl gene IDs. Thank you in advance for your answer. Kind regards, Ximena
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Hi Ximena,
I have placed this request into a ticket for easier tracking: https://bitbucket.org/galaxy/galaxy-central/issue/637
Thanks again for the suggestion,
Jen Galaxy team
On 5/31/11 6:43 AM, Jennifer Jackson wrote:
Hello Ximena,
Thank you for bring this to our attention, we are able to duplicate these same results. A "name" attribute (such as an rs number) is an important data tag and we would like to be able to have the tool retain this data if possible. Our development team is currently investigating and we will get back to you as soon as possible.
Again, we appreciate your feedback and thank you for your patience while we review potential remedies,
Best,
Jen Galaxy team
On 5/25/11 5:22 AM, Ximena Bonilla wrote:
Dear Galaxy staff, I have recently started using your tool and it has been really helpful, thank you! When using Human Genome Variation, aaChanges, I would like to keep some extra lines in the output file from either of the input files. In the tool description it says I should be able to keep them: "...chromosome, start, and end position as well as the SNP. The SNP can be given using ambiguous-nucleotide symbols or a list of two to four alleles separated by '/'. *Any other columns in the first input file will not be used but will be kept for the output*. The second input file contains..." However, I haven't found a way of actually have them in the output file. What am I missing/doing incorrectly? What I've been trying to keep by the way is rs IDs or Ensembl gene IDs. Thank you in advance for your answer. Kind regards, Ximena
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-user@lists.galaxyproject.org
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Jennifer Jackson -
Ximena Bonilla