From RNA-seq reads / alignments to GFF files

[mhadidi2002]

Hello,

Does any one know how can I create gene models (GFF files) from RNA-seq reads or alignments ?

Inputs: RNA-seq reads and reference genome, I also have the bam mapping file produced from Tophat.
I used cufflinks, but I need another tool to compare between them.

Thank you in advance.

Bes