GRIT errors and questions

[nirmala...@gmail.com]

Hi Nathan,

1. I am trying to run GRIT with paired-end RNAseq from post-mortem brain tissue data but not strand specific sequencing. Got the following error:

      "AssertionError: RNASeq reads must be stranded"

     Is it a requirement to have stranded data or is there an option to skip it?

2. I have polyaseq data for brain region but in bed format. Is there a way to pass a bed file to GRIT instead of a bam file?

3. When I use the option --use-reference-polyas I get the following error:

[akulan@helix altsplicing]$ run_grit.py --control controlFile.txt --reference Homo_sapiens.GRCh37.67.gtf --ucsc --use-reference-polyas
Process Process-2:
Traceback (most recent call last):
  File "/data/akulan/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/data/akulan/local/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/data/akulan/local/lib/python2.7/curses/wrapper.py", line 43, in wrapper
    return func(stdscr, *args, **kwds)
  File "build/bdist.linux-x86_64/egg/grit/lib/logging.py", line 13, in manage_curses_display
    curses.curs_set(0)
error: curs_set() returned ERR
Traceback (most recent call last):
  File "/data/akulan/local/bin/run_grit.py", line 4, in <module>
    __import__('pkg_resources').run_script('GRIT==1.1.3', 'run_grit.py')
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 517, in run_script
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1443, in run_script
  File "/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 515, in <module>
   
  File "/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 487, in main
   
  File "/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 449, in discover_elements
   
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1692, in find_elements
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1535, in find_all_gene_segments
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 521, in load_junctions
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 483, in load_and_filter_junctions
  File "build/bdist.linux-x86_64/egg/grit/files/junctions.py", line 231, in load_junctions_in_bam
  File "build/bdist.linux-x86_64/egg/grit/files/junctions.py", line 168, in extract_junctions_in_region
AttributeError: 'NoneType' object has no attribute 'reload'

Thank you very much.

Regards,
Nirmala