Is there an option in galaxy to identify repeat motifs? The track tandem repeat finder, also called simple repeats, provides genomic locations of STRs so the genomic sequence can be extracted. However it fails to provide the repeat motif. Is there an option in galaxy to identify repeat motifs?
This tool is wrapped in the Tool Shed for use in a production local or cloud Galaxy instance. Cloud is often the choice - be sure to review Amazon's AWS Educational grants program if you are working in an academic/research project or group (turn around for applications can be very quick).
Note that this will require some changes to the tool repository. Specifically, the option "-d data file" needs to be added to the tool wrapper. This will trigger the program to produce an output that reports the nucleotide sequence consensus (motif). More about that option is here: http://tandem.bu.edu/trf/trf.unix.help.html
Request can be made of the wrapper author to include this in the repository version itself (ideally an option on the tool's form, rather then changing the default output. Do this through the Tool Shed (requires login).
Tool Shed repository:
Galaxy local/cloud help:
There are alternate tandom repeat finding utilities in the EMBOSS tool group on the public Main Galaxy server, but I do not believe that these report the motif either.(Just ran a quick test).
Best, Jen, Galaxy team
Thanks for the prompt response!
A few follow up questions
By Amazons AWS Educational Grants program you mean the amazon.com in the link I provided right? It is for an academic research project. There are legal restrictions I need to be aware of? http://aws.amazon.com/education/
Would I need to install Galaxy locally or on the cloud for this change to work? Or would the tandem repeat finder owner upload the altered data file for public online use? Or is that up to the owner of the tool?