Hello. Can anyone explain to me what they mean by "a corresponding gtf" and where do I get it from? I'm super new to this stuff and have trouble understanding which files are which.
It also requires a transcriptome annotation (.fasta file - e.g. ensembl’s .cdna.fasta, or a prebuilt kallisto index), and a corresponding gtf.
And for salmon, in the following command:
salmon quant -i <transcriptome index> --libType A \ -o <out dir and prefix> -1 test_1.fq.gz -2 test_2.fq.gz -p <assigned threads>
Where do I get a transcriptome index for a SRPxxxxx?
Edit: I'm working with RNA-Seq data