Which reference genome to use for RNA-seq alignment HISAT2

Question

[WDW_0123]

Hi everyone,

I've only just gotten into bioinformatics and have downloaded some RNA-seq .fastq available on ArrayExpress under accession code E-MTAB-5762 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5762/samples/?s_page=1&s_pagesize=50). I want to align these files to GRCh37 reference genome with HiSAT2 and create count matrices for further analysis. There are several index files available for download on the HISAT2 website (http://daehwankimlab.github.io/hisat2/download/#h-sapiens). I'm wondering what the difference between the different indices is, and which one I should use for aligning my RNA-seq files.

should I use

• genome https://genome-idx.s3.amazonaws.com/hisat/grch37_genome.tar.gz or is
• genome_tran https://genome-idx.s3.amazonaws.com/hisat/grch37_tran.tar.gz better for RNA-seq?

Thanks for the help! Best, W

[GenoMax]

Here is what is different between difference indexes:

“genome”: HISAT2 index for linear reference
“snp”: HISAT2 index for graph reference including SNPs
“tran”: HISAT2 index for reference plus annotated transcripts
“snp+tran”: HISAT2 index for reference including SNPs, plus annotated transcripts