Problem generating gff3 exon centric annotation to run MISO

[ml439]

I would like to use MISO to extract differential alternative splicing in my rat RNA-SEQ samples, but unfortunately there are not gff3 files for Rat. Has anyone done such analysis with rat samples? could anyone help?

My problem is that Rat is generally not very well annotated, a lot of exons present in my RNA-Seq are not annotated as part of transcripts, so i have used stringtie to generate a more complete transcript annotation than the current Rn6 from enseml or UCSC. I have my annotation as a GTF file and from what I have read in the documentation I have to convert that file into a genePred format to feed it into gff_make_annotation from rnaseqlib in order to create the alternative spliced annotation gff3 files

So I took my gtf file and i have converted into genePred usig the gtfToGenePred tool:
by doing:

tools/gtfToGenePred-1 -genePredExt -geneNameAsName2 stringtie/Rat_stringtie_15june2015_merged.gtf refFlat.tmp.txt

paste <(cut -f 12 refFlat.tmp.txt) <(cut -f 1-10 refFlat.tmp.txt) > Rat_stringtie_refFlat.txt
So now i have my refFlat.txt file, unfortunately the problem is that when i try to run gff_make_annotation with my refFlat.txt it gives me an error:

File "/Applications/anaconda/lib/python2.7/site-packages/rnaseqlib/events/parseTables.py", line 56, in readTable
for col_num in range(len(header))])

Can anyone help? Would any one have done the same for their particular species that could help? Please be aware that I'm very new to RNA-seq analysis, therefore my long email and questions.