[miso-users] No generation of .miso files after run_events_analysis.py

[Yarden Katz]

Hi,

There are a couple of things to check: first, what does the MISO output say for each event as it is running?  Does it say that 0 reads map to each event?  If so, this could be caused by things like the BAM index file not being in the same directory of the BAM, or having a chromosome mismatch between the BAM and the indexed annotation.  See: 

http://genes.mit.edu/burgelab/miso/docs/#answer4

It can also mean that you've passed MISO the wrong --read-len parameter, though in later versions there's error checking for this.

Also, are you running it using MISO's cluster support (i.e. --use-cluster)?  If so, it's best to check the stdout/stderr of cluster jobs to make sure the cluster submission worked correctly.

If all else fails, please send me a subset of the BAM (e.g. for one gene or event) and the relevant gene annotation and I can take a look.  Normally this is caused by either some problem submitting jobs to cluster, or a mismatch between the BAM and the GFF headers.

Best,
  --Yarden


On Oct 9, 2013, at 9:46 AM, Beryl Jones wrote:

> Hello,
> 
> I was able to execute run_events_analysis.py on my BAM file without errors, but the resulting output directory does not contain any Psi values (no .miso files). If I then summarize the output with run_miso.py (again with no errors occurring) I get a summary file (.miso_summary) with the header information but no events (consistent with the output of run_miso.py which gives "Summarized a total of 0 events").
> 
> It seems that MISO is working properly and I've given it the appropriate files (BAM, index file, indexed GFF, etc.).
> 
> Since the issue could be with my specific GFF annotation or the BAM file itself, I was wondering how I could diagnose this problem. Is there a small sample dataset I can use to verify that MISO is working correctly?  My GFF should contain the appropriate isoform information, and I find it very unlikely that the 3321783 paired mates in my BAM file don't have expression of the isoforms present in my GFF.
> 
> Any ideas? I would be very grateful for any help!
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