I need to convert a gff3 file to gtf to use at tophat.
I tried to convert using the gffread ( came with Cufflinks), but it didn't work.
Could anyone help me with this?
Which species is this data in GFF3 format for? I wonder if a GTF is not already available out there...
Have a look at this older post. There also seems to be a Galaxy tool for this.
Gffread utility from Cufflinks is what you need. What was your command line for it that did not work?