Hi Thank you! yes, your guess is correct. Now it works. Sumathy On May 7 2011, Jeremy Goecks wrote:
Sumathy,
It sounds like you're on the right track. To visualize data for a custom build in Trackster, you need to create a custom build and use that in Trackster:
(1) using the top tabs in Galaxy, go to User --> Custom Builds; (2) add a new build with the length info as follows: <contig_name> <length>
Important note: you'll need to make sure that your contig name matches the one used in your fasta file. This is my best guess about what's causing problems for you.
(3) Create a Trackster visualization using the custom build and add your dataset.
Let us know if you have more questions/problems.
Thanks, J.
On May 6, 2011, at 10:43 PM, <puvan001@umn.edu> wrote:
Hi
I may be doing in a wrong way. I clicked trackster and I added the custom build genome. Since it is a very small genome (~2kb), I considered this as a single contig. Then I cliked "add tracks" and added my data file. But I got a message "no data for this contig. Whenever I used built in genomes I did not have any problem. I guess I am doing something wrong here.
Sumathy
On May 6 2011, Jeremy Goecks wrote:
Sumathy,
What kind of problems are you having with Trackster?
J.
On May 6, 2011, at 8:30 PM, <puvan001@umn.edu> wrote:
Hello
I was able to run RNA seq data against a custom build genome. How can I visualize the results. I tried via trackster and unfortunately I couldn't. Can you help me?
Thanks Sumathy ___________________________________________________________ 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: http://lists.bx.psu.edu/
-- Sumathy Puvanendiran Graduate student
-- Sumathy Puvanendiran Graduate student