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
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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