Tophat2 bowtie location

[lucro]

Hello all,

After installing Bio Linux and running the test data: it says that I don't have bowtie2 but bowtie2 by itself is working just fine.

What is the default location that Tophat 2 accesses Bowtie2 from? Also, is there a way to change the paths that Tophat 2 accesses it's external binaries from after Tophat 2 has already been compiled? (Samstools, Boost, Bowtie etc)?


Thanks, any constructive responses will be greatly appreciated.
I've spent a lot of time on this but I'm just hitting my head against the wall.

[dpryan]

I think it just looks in your PATH. Are the appropriate directories in there?

[lucro]

I think it just looks in your PATH. Are the appropriate directories in there?

Appropriate directories within bowtie2? Everything appears to be there. I exported the path below:

export PATH=/usr/local/bowtie2-2.2.2.0:$PATH


tophat -r tophat -r 20 test_ref reads_1.fq reads_2.fq
...
Error: Tophat requires Bowtie 0.12.9 or later

[dpryan]

What version of tophat are you using? It seems to be one that defaults to bowtie1 whereas you have bowtie2. The easiest fix would be to just upgrade your tophat version (the most recent versions should default to using bowtie2 instead of bowtie1). While bowtie1 and bowtie2 are both "bowtie", their syntax and everything is very different so you can't just arbitrarily mix and match them.

[lucro]

What version of tophat are you using? It seems to be one that defaults to bowtie1 whereas you have bowtie2. The easiest fix would be to just upgrade your tophat version (the most recent versions should default to using bowtie2 instead of bowtie1). While bowtie1 and bowtie2 are both "bowtie", their syntax and everything is very different so you can't just arbitrarily mix and match them.

I really appreciate the quick replies, dpryan.

I'm using Tophat v2.0.8 and bowtie2.2.0. I'll see if updating Tophat works.

Thanks