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Which reference genome to use for RNA-seq alignment HISAT2

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

Thanks for the help! enter image description here Best, W

reference genome alignment hisat2 rna
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updated by GenoMax GenoMax • written by WDW_0123 • WDW_0123

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
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written by GenoMax GenoMax

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