Thanks a lot for the coding effort and for sharing your script! But are you aware of this one <http://song.cvs.sourceforge.net/viewvc/song/software/scripts/gtf2gff3/>, which has been out there for quite a while? If yes, any improvements upon it? That tool works fine for me, although it does require a large amount of memory...
-- Leo
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Ensembl gtf to gff3 for tophat
I found a number of questions about finding a gff3 format file for use by tophat and couldn't find any good answers. I found a few gff3 converters but they were part of larger packages or online tools. Since I'd prefer something simpler, I wrote the attached gtf to gff converter for use with Ensembl's gtf file.
Feel free to use, modify, or distribute as you need.
Gene
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