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HISAT2 alignment issue

Hello! I am trying to do a pair end read alignment. When I run the following code --

~/hisat2/hisat2  hisat2 -x ~/hisat2/grch38 -1 ~/hisat2/astra_r1.fastq.gz -2 ~/hisat2/astra_r2.fastq.gz -S ~hisat2/ouput.sam

I get that

(ERR): "/Users/simonlab/hisat2/grch38" does not exist Exiting now ...

I know I tried many different iterations of defining the index sequence but keep getting the same error. I know I have to define the path for hisat2 to run. Any help appreciated! Thanks!

rnaseq alignment hisat2
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updated by Ram Ram • written by eleven11 • eleven11

Many alignment tools need the full path to their alignment index files with prefix. What is the output to the following commands:

file ~/hisat2/grch38
ls -lRh ~/hisat2/grch38*
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written by Ram Ram

Hello! output to file command is

/Users/simonlab/hisat2/grch38: directory

Output to ls command is

total 8797648
-rw-r--r--@ 1 lab  staff   940M Mar 12  2016 genome.1.ht2
-rw-r--r--@ 1 lab  staff   702M Mar 12  2016 genome.2.ht2
-rw-r--r--@ 1 lab  staff    11K Mar 12  2016 genome.3.ht2
-rw-r--r--@ 1 lab  staff   702M Mar 12  2016 genome.4.ht2
-rw-r--r--@ 1 lab  staff   1.2G Mar 12  2016 genome.5.ht2
-rw-r--r--@ 1 lab  staff   715M Mar 12  2016 genome.6.ht2
-rw-r--r--@ 1 lab  staff     8B Mar 12  2016 genome.7.ht2
-rw-r--r--@ 1 lab  staff     8B Mar 12  2016 genome.8.ht2
-rwxr-xr-x@ 1 lab  staff   1.5K Mar 17  2016 make_grch38.sh
(base) simonlab-imac:~ simonlab$

I have also tried running the orginal tar.gz file and get the same error. Thank you!

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written by eleven11 • eleven11

1 answer

You need -x ~/hisat2/grch38/genome. The manual says:

Main arguments

-x <hisat2-idx> The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2_INDEXES environment variable.

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written by Ram Ram

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