Anyone Tried MISO with Posted GFF files?

[12jrowley2]

I am trying out the Burge lab's MISO program for isoform analysis. I want to use the mm9 file posted on their website, but within the mm9 folder are many subfolders with different pickled GFF annotations, I can't seem to get MISO to like any of these files. Which files do I feed MISO? Anyone else have this trouble, or have better experience using their own indexed alternative events file? Anyone gotten MISO to work?

[hjanime]

Yh, I have tried their hg18 GFF annotations for alternative splicing analysis, it works well.

[12jrowley2]

Miso

good to hear it is working for you - did you run it using the TandemUTR or A3SS/A5SS indexes? for the input file I navigate to the mm9_alt_events/home/yarden/sugarman/gff-events/mm9/pickled/TandemUTR folder -within that folder are the .shelve file and the individual chromosome folders containing pickle files. Trying to run from this folder gives me errors. What do I use as my input file? test_miso.py gives me an OK. Do I need to prepare the pickled files?
thanks, any help is appreciated.

[hjanime]

I tried all the events including TandemUTR and A3SS/A5SS indexes, I think you can use their scripts and gff files to generate the pickled files ,not the final annotation files they already provided.

[12jrowley2]

MISO - got it thanks

Thanks, I got it working now.

[ozs2006]

Miso vs. cufflinks

For miso users: What is the feature that distinguish miso from cufflinks, and helped you take miso as your favorite tool?