SpliceGrapher help

[RHous]

I have just begun using the program SpliceGrapher to visulaize alternative splicing events from my RNA seq experiment. However I am having trouble figure out the scripts to use in order to generate the read depths graph and splice junction with read support graph. I am also new to using linux so any and all help would be appreciated.

Thanks

[CompBio]

There are two SpliceGrapher tools that allow you to view read depth and splice junctions. The view_splicegraph_multiplot.py script is an older script that allows you to view gene models, splice graphs, splice junctions and read depths on your screen. It also allows you to send the figure to a file, but in general it is easier to use the plotter.py script for that purpose.

The plotter.py script was designed for generating publication-quality figures. It uses configuration files so that you can set plot parameters precisely and consistently.

These tools are still evolving as we get requests and suggestions from users. If you have more specific questions about viewing or plotting splice graphs, please contact us at the e-mail addresses provided in the SpliceGrapher documentation.