[miso-users] questions on using sashimi-plot

[Gao, James (NIH/NCI) [E]]

Hi Yarden,

I have a question and an error message to ask for your help when I used the sashimi-plot utility.

First, the pe_utils.py --compute-insert-len seems to use too much memory. For a 20 million reads PE bam file, it took over 50G memory. Is this real? Or is a way to just sample a subset of the data.
Second, when I used the plot.py --plot-insert-len, I got the following error message:

Thanks for your help.


Traceback (most recent call last): File "/usr/local/src/MISO/misopy/sashimi_plot/plot.py", line 293, in <module> main() File "/usr/local/src/MISO/misopy/sashimi_plot/plot.py", line 271, in main plot_insert_len(insert_len_filename, settings_filename, output_dir) File "/usr/local/src/MISO/misopy/sashimi_plot/plot.py", line 149, in plot_insert_len settings_filename=settings_filename) File "/usr/local/src/MISO/lib/python2.7/site-packages/misopy/sashimi_plot/Sashimi.py", line 41, in __init__ no_posteriors=no_posteriors) File "/usr/local/src/MISO/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_settings.py", line 83, in parse_plot_settings settings[option] = json.loads(config.get(section, option)) File "build/bdist.linux-x86_64/egg/simplejson/__init__.py", line 385, in loads File "build/bdist.linux-x86_64/egg/simplejson/decoder.py", line 402, in decode File "build/bdist.linux-x86_64/egg/simplejson/decoder.py", line 418, in raw_decode simplejson.decoder.JSONDecodeError: Expecting object: line 3 column 1 (char 26)