Do I have to use index with trans information for RNA-seq alignment by Hisat2?

Question

[ben.kunfang]

Hi,

I am a newbie in RNA-seq analysis. I would like to use HISAT2 for RNA-seq alignment. In HISAT2 website, I found that pre-built index have genome_snp_tran of grcm38 and genome of mm10. I was wondering if I could use mm10 genome for RNA-seq alignment? If I cannot, I was wondering how can build an index for mm10 RNA-seq alignment. Thanks!

Best, Kun

Answer 1

[Istvan Albert]

HISAT2 was designed to align transcriptomic reads to genomes, thus you can use the genome file.

[ben.kunfang]

Thanks a lot! In this case, I can directly use the pre-built mm10 index for RNA-seq alignment without trans in it, right? If you don't mind, can I ask why hisat2 offers the trans and snp index for grcm38 if it can handle the transcriptomic alignment by itself? Thanks again!

[Istvan Albert]

The tool can align against transcriptomes as well, but in those cases, one would not be able to detect a new splice variant and most pipelines would work differently.