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Old 06-03-2017, 04:34 AM   #1
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Location: Germany

Join Date: Jun 2017
Posts: 1
Default HISAT2 executable


I am trying to use HISAT2 ( to do alignments and downstram processing.
The problem that I encounter is that I am not able to get a hisat executable file after running the
command (I am on Ubuntu 16.04).
on the downloaded binary (or the source) file gives me all the other required executables (hisat2-align-s, hisat2-align-l, hisat2-build, hisat2-build-s, hisat2-build-l, hisat2-inspect, hisat2-inspect-s and hisat2-inspect-l) but not hisat2 which is required in the alignment step.
May be I am just missing some small point here but any help will be great.

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Old 06-03-2017, 11:46 AM   #2
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Location: uk

Join Date: Mar 2009
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You don't need to run 'make' if you download the binary, only if you are trying to build from the source code.

What version of HISAT2 are you using?

I just downloaded the Linux binary for version 2.0.5, unzipped the file, and hisat2 is present, along with the other hisat2 programs.

Last edited by mastal; 06-03-2017 at 11:56 AM.
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