[miso-users] Extract genomic coordinates from alternative exons?

[Yarden Katz]

Hi,

MISO does not include the full coordinates because in the case of multiple isoforms, it can get incredibly large (think of the space required to describe the coordinates of each exon making up each isoform), but it's guaranteed that each event name -- meaning the ID= of the GFF -- is unique.  So all you need to do is lookup the events of interest in your GFF to find out everything you'd like about their structure/coordinates.  The information you'll want to fetch will depend on the events of interest and what your downstream analysis is, so there isn't a standard solution to this.

For parsing GFF: There are many GFF parsing libraries in Python, C, Ruby and other languages.  If you use Python, you can also use MISO's GFF parser, by doing:

import misopy
import misopy.gff_utils as gff_utils

And then using the features in "gff_utils".  However, there are other parsers out there which are faster and probably better.  Ryan Daler has a parser written using Cython:

https://github.com/daler/gffutils

I have not used it but it looks promising & fast and might do what you need.

Best, --Yarden



On Jan 18, 2013, at 10:17 AM, Li Shen wrote:

> Has anyone tried to extract genomic coordinates from MISO filtered
> results in batch? Each MISO alternative splicing event corresponds to
> one or more exons that show differential expression. It would be
> fairly interesting to extract all of them into two files, e.g.
> miso_up.bed and miso_down.bed for each type of splicing events and
> study their common features. By looking through MISO's output and
> annotation database, it seems this task requires parsing the GFF files
> and then find the IDs that are in the filtered lists.
> 
> I'm wondering if anyone has done this before. Would you like to share
> your scripts?
> 
> Thanks,
> 
> --
> Li Shen, Ph.D. Computer Science
> Assistant Professor
> Department of Neuroscience
> Mount Sinai School of Medicine
> One Gustave L. Levy Place, Box 1065
> New York, NY 10029
> Phone: 212-659-8622 (office)
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