align using file.ht2

Question

[m90]

I downloaded in my terminal indexed file of UCSC hg19 and when I uncompressed it, I found two files genome.5.ht2 and genome.8.ht2. Every time I want to align my samples at indexed file this error show up

[e::bwa_idx_load_from_disk] fail to locate the index files command exited with non-zero status 1

So, my question is: Which one of two files I should use and how use file.ht2 in alignment?

Answer 1

[Wakala]

You should put the index in a separate folder and when you use hisat2 you should enter the index folder not the index file, just like this:

hisat2 -p 10 -x dir/genome -1 fq -2 fq

[m90]

it didnt work still have the same problem because uncompressed folder has two files that i dont know which one of them i should assign in my path

[m90]

(ERR): "/home/ngs/workdir/hg19" does not exist Exiting now ...

[Wakala]

You can try /home/ngs/workdir/hg19/genome. Also, when you use a software, read it document is a good idea, just use command 'hisat -h', and it will solve most of your confusion.

[Wakala]

<ht2-idx> Index filename prefix (minus trailing .X.ht2).

[Wakala]

[Wakala]

This is wha I downloaded before when I used hisat2 in sequence alignment.