[miso-users] sashimi_plot without miso

[Cara Lee Ann Ruble]

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
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[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

Post by Cara Lee Ann Ruble
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
<image001.jpg>
CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
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