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Old 07-16-2013, 10:06 AM   #1
Hubertus
Junior Member
 
Location: Sweden

Join Date: May 2013
Posts: 2
Default Miso/Sashimi python error

Hello! New to forum and bioinformatics...

I've run RNA-seq quite deep (100-PE, ~200 M reads/samples) on primary tumors, looking at splice events with MISO / Sashimi.

GFF annotations are indexed from Ensembl hg19.

Upon running shashimi plot on my local desktop (Mac OS) I encounter an index error after some time:

python plot.py --plot-event "ENSG00000XXXXX" /Applications/misopy-0.4.9/misopy/indexed_SE_events/ sashimi_plot_settings.txt --output-dir S
ashimi_1

Traceback (most recent call last):
File "plot.py", line 340, in <module>
main()
File "plot.py", line 334, in main
plot_label=plot_label)
File "plot.py", line 154, in plot_event
plot_label=plot_label)
File "/Users/name/Library/anaconda/lib/python2.7/site-packages/misopy-0.4.9-py2.7-macosx-10.5-x86_64.egg/misopy/sashimi_plot/plot_utils/plot_gene.py", line 687, in plot_density_from_file
plot_title=plot_title)
File "/Users/name/Library/anaconda/lib/python2.7/site-packages/misopy-0.4.9-py2.7-macosx-10.5-x86_64.egg/misopy/sashimi_plot/plot_utils/plot_gene.py", line 257, in plot_density
miso_file = os.path.expanduser(miso_files[i])
IndexError: list index out of range

Anyone having experience with this? Solution?

All the best,

Hubertus
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Old 03-20-2014, 12:57 PM   #2
xguo
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Location: Maryland

Join Date: Jul 2008
Posts: 48
Default

Has anyone here successfully run sashimi_plot? I got an error below when running sashimi_plot:

NameError: global name 'subplot2grid' is not defined

The command is like this:
"sashimi_plot --plot-event "chr12:100551517-100551306:-@chr12:100551034-100550943:-" RI_indexed/ sashmi_plot_settings.txt --output-dir plot"

Any insight is greatly appreciated.

thanks
Xiang
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