Need help with Reference sequence preparation using RSEM

[DuRoss]

Hi everyone,

I have mapped my reads using bowtie2 and now ready to proceed to further downstream analysis. I am hoping to use RSEM tools for quantification of transcript abundance with a reference genome but I only have a .gff format for my reference genome annotation and I think 'rsem-prepare-reference' command would require a .gtf file format?

I am not sure if there's a way to convert a .gff to gtf? I also have the gene annotation in text format btw.

Looking forward to hear your advise. Thank you very much for your help!

Cheers,
Ross