[miso-users] sashimi_plot without miso

[Yarden Katz]

Hi Cara,

Not specifying the miso_files or specifying any directory that does not contain MISO files (or a value like "None") should work.  What error you get when you try one of these?  

Best, Yarden

On Jul 31, 2015, at 1:40 PM, Cara Lee Ann Ruble <ruble_cara_lee_ann at lilly.com> wrote:

> Hello,
>  
> I am new at the command line sashimi_plot.  The latest publication would indicate that MISO output is now optional for input into sashimi_plot.  I am not clear on what the proper changes to the sashimi_plot_settings.txt would be.  Using the example provided in the http://miso.readthedocs.org/en/fastmiso/sashimi.html, I am able to generate the plot with using the MISO output provided.  I have tried a number of ways to not provide the MISO output and still generate the plot: I have tried commenting out the miso_files line, leaving the [] list blank, and deleting this whole section.  All of these approaches lead to error messages without a plot.
>  
> Do you have any suggestions or examples of what the sashimi_plot_settings.txt should be for just using the GFF and BAM?
>  
> Thanks!
> Cara
>  
> Cara L. Ruble
> Consultant Biologist, TTx Neuroscience
> Eli Lilly and Company
> Lilly Corporate Center
> Indianapolis, IN 46285 U.S.A.
> 317.651.5344
> rubleca at lilly.com | www.lilly.com
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