Dear All,

I’m making a command line for HISAT following the manual instruction. 
What is not clear to me is how to use the genome index files.
I downloaded from HISAT website the reference genome (genome.1.ht2… until genome.8.ht2)

My question is how to use this? the manual says “any of the index files up to but not including the final .1.ht2” 
can I just pick one, insert into the line command and remove thee others from the folder?

My command would be like

    hisat2 -q -x genome -1 mymate1.fq -2 mymate2.fq -S -o resultpath

I know it's not correct.. but can you kindly help me to fix it?

Thank you 
what the manual is trying to explain to you with 

> “any of the index files up to but not including the final .1.ht2”

is that you need to provide the file name you used for the index but omit the '`.1.ht2`' part from it. So using simply 'genome' as you did in your example is correct (given the index names you provided).

and, no, you can not remove the others from your directory, the software needs all of them to work. 


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EDIT: to resolve all issues with the posted cmdline, you will need to add a correct value (== a filename to write the sam output to) for the `-S` parameter.