Why do I need the command perl to run bowtie2?

[TofuKaj]

Dear all great helpers,

I'm very naive to both unix, perl and RNAseq. I've download bowtie2-2.2.5 to my ~/bin folder and install it. I set path " export PATH="$PATH:~/bin" "

The problem is I cannot use command "bowtie2". It returns me :

command not found: bowtie2

The only way I can use bowtie2 is to write :

perl ~/bin/bowtie2-2.2.5/bowtie2

I also notice that my tophat-2.0.14 cannot detect bowtie2, as well. I'm wondering it should be due to the same problem.

Would you please suggest me what to do step-by-step? I must confess I'm very desperate to figure out what to do next.

Note : My perl command is in usr/bin/.

[dpryan]

If bowtie2 is under ~/bin/bowtie2-2.2.5, then you need to "export PATH=$PATH:~/bin/bowtie2-2.2.5".

Doing this will also fix tophat2.

[TofuKaj]

If bowtie2 is under ~/bin/bowtie2-2.2.5, then you need to "export PATH=$PATH:~/bin/bowtie2-2.2.5".

Doing this will also fix tophat2.

Thank you very much, it helps bowtie2
However, my tophat2 still cannot see it Would you please suggest me further what I'm missing here (I'm thinking about coppying all my bowtie2 function in tophat's bin)?

Thank you very much in advance,
Kaj

[dpryan]

If you can execute bowtie2 by simply typing

bowtie2

then tophat2 should be able to see it as well.

[TofuKaj]

If you can execute bowtie2 by simply typing

bowtie2

then tophat2 should be able to see it as well.

I try with the example data. My tophat still cannot see bowtie2.
Of note, all my bowtie1 commands are in usr/bin/. Can this be the problem?

kaj@kaj-Lenovo-G400[test_data] tophat -r 20 test_ref reads_1.fq reads_2.fq [ 4:16PM]

[2015-04-17 16:16:20] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2015-04-17 16:16:20] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 1.0.0.0
[2015-04-17 16:16:20] Checking for Samtools
Samtools version: 0.1.19.0

[dpryan]

I would start by upgrading the version of tophat, you have one from 2013 that isn't even compatible with the current bowtie2 version (actually, I don't know if the most recent version of tophat2 is compatible with the most recent bowtie2, though presumably it is).

BTW, you might just use hisat instead, it's faster.

[TofuKaj]

I would start by upgrading the version of tophat, you have one from 2013 that isn't even compatible with the current bowtie2 version (actually, I don't know if the most recent version of tophat2 is compatible with the most recent bowtie2, though presumably it is).

BTW, you might just use hisat instead, it's faster.

Your answer just ring my suspects! After trying several update bowtie2, I've found only bowtie2-2.1.0 works
I've waste one week with this knowledge

[GenoMax]

Latest versions of TopHat, bowtie2 and Cufflinks would be the way to go. They are all compatible with each other.

BTW: TopHat still requires old samtools (0.1.19). It is actually included in the source download.

[TofuKaj]

Latest versions of TopHat, bowtie2 and Cufflinks would be the way to go. They are all compatible with each other.

BTW: TopHat still requires old samtools (0.1.19). It is actually included in the source download.

Yes, you r right. I've just re-install everything and it works with works fine with the test_data.