[miso-users] Miso annotation

[Kazuyoshi Ishigaki]

Dear all,

I am using Miso for exon centric analysis using annotation file 
created by authors. My RNA-seq data is 150bp, paired-end.
I found that there were many (0,0) fragments in my output file.
I carefully checked those fragments in genome browser, and realized 
that those reads are overhanging to more than 3 exons.
Because there are only two flanking exons in their annotation, 
fragments overhanging more than 3 exons are judged to be incompatible 
with either isoform.
In Miso manual, they said,
"Note that we only use the two flanking exons in this annotation, 
but one could modify the annotation to include arbitrarily 
many flanking exons from the transcripts." 

I am quite new to bioinformatics and I have trouble creating custom
annotation file with many flanking exons.
Is there anyone who already created such files and kind enough to
share with me ??


Thanks,
Kazu