[miso-users] run_miso.py problem

[Yarden Katz]

Hi Tiffany,

We recently had an introduced a feature that caused MISO to run extra long on certain events -- this feature was turned off in the latest version in GitHub.  But it is not yet made into a stable release.

Could you please try the GitHub version and see if the problem goes away?

Alternatively, you can send me the BAM file containing just the reads for this RI event and I will test it.

Thanks.

Best, --Yarden




On Jul 24, 2012, at 11:45 PM, Tiffany wrote:

> 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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