[miso-users] New and expanded alternative event annotations for MISO

[Yarden Katz]

Hi all,

We've created a new set of MISO alternative event annotations for the human and mouse genomes. These annotations are still being tested and we'd like your input.  These annotations (labeled "version 2.0") are available here:

http://genes.mit.edu/burgelab/miso/docs/annotation.html

These annotations contain on average many more events than the previous annotation. For example, the old mm9 annotation for skipped exons (SE events) contained ~8000 skipped exons, while the new set contains ~14,000.  Similarly, the old retained intron (RI) annotation had ~1200 events, while the new one has ~3100 retained intron events.

The new annotation includes basic gene information (Ensembl gene ID, RefSeq gene ID, and gene symbol), available in the optional attributes of the GFF files. 

Comments on the annotation are welcomed. Our goal was to create a conservative, high confidence set of events that are reliably alternative, rather than the most inclusive RNA-Seq/EST based annotations, which could have considerable noise in them.  

The code used to generate these is open source (part of rnaseqlib software) and in principle works with any UCSC-available genome.

Thanks to Ryan Dale for his software gffutils which was instrumental in creating these annotations.

Best, --Yarden