I am trying to determine differential expression between two test conditions - in rat. The first step would be to map the sequencing data to a rat reference of some sort, and I would like to use HISAT2 (locally installed on my machine) along with the Ensemble rat genome.
Which reference file(s) do I map against?
1) Do I use the hisat2 index for rn6 as is: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/rn6.tar.gz ?
2) Do I need to generate my own hisat2 index from the Ensemble reference genome (ftp://ftp.ensembl.org/pub/release-86/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna_sm.toplevel.fa.gz) and annotations file (ftp://ftp.ensembl.org/pub/release-86/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.86.gtf.gz)