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

[Li Shen]

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)