[miso-users] questions on using sashimi-plot

[Yarden Katz]

Hi James,

See below for replies:

On Feb 10, 2012, at 11:01 AM, Gao, James (NIH/NCI) [E] wrote:

> 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.

You're right that this can be optimized.  The explanation is that in order to compute the insert lengths, the read pairs must be paired.  Right now, the code naively loads all of these reads into memory in order to pair them up, so the memory consumption is roughly on the order of the number of reads landing in constitutive exons (which is quite huge.)

It's on my list to optimize this, since it definitely should not require this much memory, so if this is of pressing use to you I can prioritize a fix to this.


> Second, when I used the plot.py --plot-insert-len, I got the following error message:

It looks like the error is in the config file parsing.  Could you please send me your sashimi plot settings file, the exact command you ran it with, and the version of misopy you're using?

It would also help if you send me your .insert_len file.  

Thanks, --Yarden

> 
> 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.JSONDecodeErr!
> or: Expecting object: line 3 column 1 (char 26)
> 
> 
> 
> 
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