HTSeq-count: gene models/transcripts are in FASTA format not gtf/gff

Question

[sbrashidx]

I've generated .SAM files with RNA-seq reads aligned to a reference genome using STAR. I ultimately want to pull out differential expressed genes from my dataset.

I've chosen to use HTSeq-count to generate count files to ultimately use in either DEseq2 or EdgeR. It seems I need to provide a gff/gtf file with transcripts or gene models. I have access to both the gene models and transcripts for the genome, but both files are in FASTA format.

What can I do to solve this issue? Is there another program, besides HTSeq I could use to generate count files?

Thank you so much!

[cschu181]

You could use kallisto and then import into DESeq2 via tximport. The DESeq2 vignette at bioconductor has an example for this.

[elisheva]

Which reference genome did you use? I am sure you can get the matching gtf/gff files somewhere.