[miso-users] new mouse genome annotation for alternative cleavage and polyadenylation events

[Charizanis,Konstantinos]

Thank you Yarden for the fast reply!
This is the error it reports:

Traceback (most recent call last):
  File "/apps/python/2.7.3/bin/filter_events.py", line 406, in <module>
    main()
  File "/apps/python/2.7.3/bin/filter_events.py", line 403, in main
    apply_both_samples=options.apply_both)
  File "/apps/python/2.7.3/bin/filter_events.py", line 104, in multi_filter
    apply_both_samples=False)
  File "/apps/python/2.7.3/bin/filter_events.py", line 265, in filter_events
    for bf in bayes_factor:
TypeError: 'float' object is not iterable


I understand what you say. To clarify something, does this mean that the 5 different values for each tab (for example diff: -0.00,0.00,-0.03,-0.24,0.27) is the value for each one of the new annotated 3'UTR? 
I already performed the analysis with the older annotation (two events per gene) but I got excited to get a more complete view of the polyA changes with the new annotation.
I guess I won't be able to use it since I cannot filter out the results, unless I break it down in different columns and try to run it that way (probably I'm wrong). 

Thank you again!


-----Original Message-----
From: Yarden Katz [mailto:yardenny at gmail.com] On Behalf Of Yarden Katz
Sent: Monday, January 07, 2013 4:20 PM
To: Charizanis,Konstantinos
Cc: miso-users at mit.edu
Subject: Re: [miso-users] new mouse genome annotation for alternative cleavage and polyadenylation events

Hi Konstantinos,

See comments below:

On Jan 7, 2013, at 3:31 PM, Charizanis,Konstantinos wrote:

> I used the new annotation (Bin Tian DEC 2012)  to do a previous analysis but I have the following problem. Miso works up to the comparing sample step. After that it gives an error when I try to filter the results.
> I went and viewed the Bayes factors file output of the comparison and it doesn't make any sense. I'm copied the first couple rows.
>  
>  
> event_name      sample1_posterior_mean  sample1_ci_low  sample1_ci_high sample2_posterior_mean  sample2_ci_low  sample2_ci_high diff    bayes_factor   etc.
>  
> Zyx:42307851    0.01,0.03,0.05,0.48,0.44        0.00,0.01,0.01,0.15,0.02        0.01,0.05,0.08,0.90,0.77        0.01,0.03,0.08,0.73,0.16        0.00,0.01,0.04,0.44,0.01        0.01,0.04,0.11,0.89,0.45    0.00,0.00,-0.03,-0.24,0.27      0.00,0.03,0.13,0.95,0.93        'Zyx:42307851.1.0','Zyx:42307851.2.0','Zyx:42307851.3.0','Zyx:42307851.4.0','Zyx:42307851.5.0'

Note that the new Tian annotation is a *multiple isoforms* annotation, meaning it annotates two or more 3' UTRs per gene.  The output you show above is the correct format for a gene with multiple (in this case, five) isoforms.  You get a Psi value for each isoform, a DeltaPsi for each isoform, etc. 

You never said what the error you got was -- but the built-in filtering feature in MISO is only defined for two-isoform events, which is probably why it did not work.

You could use the new Tian annotation and modify your analyses to account for the fact that some genes have more than 2 isoforms.  Otherwise, you could use the old annotation, or select only genes with two isoforms from the new Tian annotation if those are the genes that interest you.

>  
>  
> I also checked the indexed gff annotation and it looks different from the previous annotations that exist on the MISO website.  

Yes, it's a totally different annotation, and the older one is still available.  

Best, --Yarden

> Any input or ideas would be much appreciated.
> Thank you
>  
> Konstantinos
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