HISAT2 indexing hg19 reference transcriptome

Question

[Morris_Chair]

Hello everyone,

I want to index the hg19.fa for hisat2 usage, I know that the generic command line is

hisat2-build [options]* <reference_in> <ht2_base>

I m slowly getting familiar with commands but now I wanted to ask you what should I use in the [options] ? in the manual there are severals but I don’t know which one is the right to use in this case/

Can be ok this one?

Hisa2-build hg19.fa hg19-indexed

Where hg19-indexed is my output

Or, Is there a website where I can download an indexed and ready to use ?

Thank you

[ATpoint]

Hisat2 main page (first hit on google) on the right of the page, scroll down a bit, will find premade indices. If you want to do it yourself you'll need to include a splice site file (indicating where splicing takes place in the genome/transcriptome. Please use google and the search function on why this is important. Has been asked/discussed man times before.

Build a HISAT2 index of hg 19

hisat2-build indexing produces more than 8 output files