To pull in annotation and view/use it in Galaxy, use the "Get Data" tool
and either extract from one of the listed databases or load a local file.
The primary source for known miRNA data would be: http://www.mirbase.org/
Pseudogenes and other longer non-coding mRNA data can be found in
other major genome annotation repositories.
For Human and other vertebrate species, the UCSC Genome Browser would be
a good place to review tracks based on the the sources above. These can
be easy imported with the "Get Data -> UCSC main or BX main" tool.
If you would like more help with a particular genome or dataset, please
let us know,
On 12/2/10 7:35 AM, Abhay Krishna wrote:
I have an intuitive feeling, It will be possible to do it in Galaxy,
to be precise:
I want to find all miRNA targets at whole genome level (These targets
should be transcribed but not translated), in other words pseudogenes
and other non coding rna.
Any ideas? How to get this.
galaxy-user mailing list