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bowtie2 tophat2 vesion
total 28852

drwxrwxr-x. 5 pielab pielab     4096 Feb 27  2013 bowtie2-2.1.0
-rw-rw-r--. 1 pielab pielab 15631689 Feb 27  2013 bowtie2-2.1.0-linux-x86_64.zip
drwxr-xr-x. 6 pielab pielab     4096 Sep  3  2011 samtools-0.1.18
-rw-rw-r--. 1 pielab pielab  1372160 Sep  3  2011 samtools-0.1.18.tar
drwxrwxr-x. 2 pielab pielab     4096 Jun 29  2013 tophat-2.0.9.Linux_x86_64
-rw-rw-r--. 1 pielab pielab 12523601 Jun 29  2013 tophat-2.0.9.Linux_x86_64.tar.gz

I have above tools and when I run tophat, it shows me this problem.

[2015-08-11 21:35:16] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2015-08-11 21:35:16] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

Do I have to download other versions? which is the proper version for the tophat?

next-gen-sequencing rna-seq
• 4,982 views • link
updated by Ram Ram • written by Lee yujeong • Lee yujeong

can you call bowtie2 from shell? The path is set for bowtie2?

• 1 views • link
written by AndreiR AndreiR

I called bowtie2 in .bash_profile

$ vi .bash_profile
export PATH=$HOME/path/to/bowtie2/bin/:$PATH
$ source .bash_profile
• 1 views • link
updated by Ram Ram • written by Lee yujeong • Lee yujeong

can u just type bowtie2 in command line and let us know if you see all the bowtie2 options ?

• 1 views • link
written by GouthamAtla GouthamAtla

you means

export PATH=$HOME/path/to/bowtie2-2.1.0/bowtie2/bin/:$PATH

I wrote that command in .bash_profile and then exit the vi edit

$ source .bash_profile
• 1 views • link
updated by Ram Ram • written by Lee yujeong • Lee yujeong

open terminal/command line, type bowtie2 and press enter. What you see there ?

• 1 views • link
written by GouthamAtla GouthamAtla

hi~

type bowtie2 and bowtie2 path in terminal

$ bowtie2
-bash: bowtie2: command not found
$ /path/to/bowtie2-2.1.0/bowtie2
No index, query, or output file specified!
Bowtie 2 version 2.1.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <sam>      File for SAM output (default: stdout)
.
.
.
• 1 views • link
updated by Ram Ram • written by Lee yujeong • Lee yujeong

This

$ bowtie2
-bash: bowtie2: command not found

shows that the PATH is not set properly. Which OS are you using ? You should see options of bowtie2 when you type bowtie2.

• 1 views • link
updated by Ram Ram • written by GouthamAtla GouthamAtla

thank you

I use Linux os .. I try to download Linux version

• 0 views • link
updated by Ram Ram • written by Lee yujeong • Lee yujeong

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