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4.3 years ago
sbrashidx
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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!
You could use kallisto and then import into DESeq2 via tximport. The DESeq2 vignette at bioconductor has an example for this.
Which reference genome did you use? I am sure you can get the matching gtf/gff files somewhere.