[miso-users] run_miso.py problem

[Tiffany]

Dear Yarden,   
 
 
 When using MISO to analysis our RNA-Seq data, we found run_miso.py of miso_0.4.3 would be in the satus of computing psi for nearly 70 minutes for just one event (the gff file was made by our scripts). And the event involved is attached here.
  
 The command was:
 python /media/disk2/tli/program/program_install/misopy-0.4.3/lib/python2.6/site-packages/misopy/run_miso.py --compute-gene-psi "chr6:39239911:39240397:- at chr6:39239364:39240397:-" "/media/disk2/qrai/module/dsg_module/non_miso/zfish_out/index/RI/chr6/chr6:39239911:39240397:- at chr6:39239364:39240397:-.pickle" /media/disk2/tli/module/other_test/miso_nonmodel/non_miso/nonmiso_out/s1/accepted_hits.sorted.bam /media/disk2/tli/module/other_test/miso_nonmodel/non_miso/nonmiso_out/s1.RI_aly --read-len 115  --paired-end 260.0 50.0 --settings-filename /media/disk2/tli/program/program_install/misopy-0.4.3/lib/python2.6/site-packages/misopy/settings/miso_settings.txt >> /media/disk2/tli/module/other_test/miso_nonmodel/non_miso/nonmiso_out/s1.RI_aly/batch-logs/batch-0-07-24-12_21:15:16.log;
  
 So please help with the problem. Look forward to your reply. Thanks in advance.
  
 
 
 Yours sincerely,
  
 
 
 Tiffany Lee
  
  
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