Hi, my project requires me to analyze the differential expression of mRNAs, lncRNAs, and miRNAs. So to align the raw fastq files I have, I need to align the reads to a reference genome. For the same, HISAT2 provides its own pre-built indexes based on GRCh38 (ensembl release 84 or something). I feel like it is old at this time and I want to use ensembl release 105. Now I am unsure about which file to use to build a new index. I was previously using genome_tran index available at http://daehwankimlab.github.io/hisat2/download/. So if I am to make my own index, which file should I use? (from ensembl release 105 http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/)
- cdna/Homo_sapiens.GRCh38.cdna.abinitio.fa.gz
- cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
- dna_index/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Also, can someone provide me the full codes required to build it.
Much appreciated, Thank you!
So, the default genome_tran index for hisat2, which is based on ensembl's release 84 be good and relevant enough?