What files (fasta, GTF) do I need for RNA seq analysis
I am very new to programming in general, and I’m trying my best to teach myself R for analyzing RNA-seq data we have.
I am using this guide and have gotten to the step where I need to align to mapped reads. however, when I use the GTF file to align my reads, I don’t get any alignments.
I suspect that I used the wrong file for the genome alignment, the wrong GTF, or both.
Can someone please confirm or deny?
My RNA seq data is from mouse samples. I used this link to download Mus_musculus.GRCm39.104.gtf.gz, and the reference genome I used is the cDNA sequence from here
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