Hi guys
May I know where can i reference more about writing an application that is able to retrieve the read mapping of a specific gene, given the gene ID or the name of the gene.
I am planning to write it in python anyway...
Regards,
Julius
Do you want to have the read-count for a specific gene?
Hey Bjoern
Yes I do. Do you have any article which i could review? or better if there is any source available?
Regards,
Julius
Not really, but have a look at HTSeq-count. This tool is part of the ToolShed and can be installed into any Galaxy instance.
Thanks for the advice Bhoern, however I am being tasked to develop an application by leveraging Galaxy's API. So was wondering which areas can i explore into..
A good start to read about Galaxy's API is the following documenation: http://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html
However I am not sure how you plan on using Galaxy's API without being interested in the tools that will perform the analysis steps. Galaxy itself is an engine to run tools. Without the tools you can't do much.
Thanks Martin
Is there currently a script that could retrieve the read mapping results of a specific gene, with given gene ID or gene name?
Regards,
Julius
Hello, The solution here is most likely a Workflow that utilizes the tool that Bjoern mentions. Create the Workflow on your server (once the tool is loaded, or you wrap/load your own tool that perform the read->transcript mapping), add in the other tools/steps needed (input reference data, mapping transcript to gene names/IDs from the source you want to use, etc.). Then that Workflow can be executed through the API. Thanks, Jen, Galaxy team
