Jiannong, Hans is on right track. You can indeed visualize your data using Trackster, Galaxy's genome browser; Trackster is available via the Visualization tab. Here are the steps needed to visualize your dataset: (1) Use the [FASTA Manipulation --> Compute Sequence length] tool to compute lengths the contigs in your build; (2) if there are spaces in your contig names, you'll need to use only the characters before the first space as contig names because this is what the mapping tools do; use [Text Manipulation --> Convert delimiters to TAB] and then [Text Manipulation --> Cut ] to cut the first and last column from the dataset; now you should have a file in the form <contig_name><tab><contig_length> (2) Create a custom build: (a) User tab --> Custom Builds; (b) scroll to the bottom, enter a name and key for your build and copy in the contig names and lengths you created in steps (1) and (2); (3) Set the dbkey for the dataset(s) that you want to visualize by clicking on the pencil icon for each dataset and selecting your custom dbkey. (4) Use the Trackster icon next to a dataset--see attached screenshot--and insert the dataset into a new browser. Let us know if you have any problems. And, yes, we're working to make this process much easier. Best, J. On Aug 4, 2011, at 3:13 AM, Hans-Rudolf Hotz wrote:
Hi
Assuming you know the length of your contigs, you can add them as a "custom build".
Click on: 'Visualization -> 'New Track Browser' -> 'Add a Custom Build'
Hope this helps.
Regards, Hans
On 08/04/2011 01:51 AM, vasu punj wrote:
IGV should allow you to do this but not sure about trackbrowser in Galaxy. Vasu
--- On Wed, 8/3/11, Jiannong Xu<jxu@nmsu.edu> wrote:
From: Jiannong Xu<jxu@nmsu.edu> Subject: [galaxy-user] visualization To: "galaxy-user@lists.bx.psu.edu"<galaxy-user@lists.bx.psu.edu> Date: Wednesday, August 3, 2011, 6:03 PM
Hi Jen,
I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization?
Thanks
John Xu NMSU
___________________________________________________________ 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:
___________________________________________________________ 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:
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:
