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align using file.ht2

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?

ht2 hisat2
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updated by Ram Ram • written by m90 • m90

1 answer

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
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updated by Ram Ram • written by Wakala • Wakala

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

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written by m90 • m90

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

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written by m90 • m90

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.

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written by Wakala • Wakala

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

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written by Wakala • Wakala

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

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written by Wakala • Wakala

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