Bowtie 2.2.0

[giorgifm]

Dear all,

I just installed the newest version of Bowtie2 (2.2.0)

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

The version appears to be incompatible with Tophat 2.0.10 (it cannot find bowtie2, even if it is in the PATH).
The problem arises from the fact that the executable bowtie2-align disappeared, as two executables substituted it: bowtie2-align-l and bowtie2-align-s

The Tophat problem can be fixed by putting in the path a link to bowtie2-align-l named bowtie2-align

My question is: what are the two versions -l and -s? The difference is not documented anywhere, but it's present also in the bowtie2-build executables.

[dpryan]

-l is meant for "large genome" support. One of the new features in bowtie2 2.2.0 is support for arbitrarily large genomes. Yeah, you have to look through the perl code in bowtie2 to find this out.

[giorgifm]

I thought so. Thank you dpryan!

[rajj]

Is there a downside to using the "-l" version on small genomes?

[genome1]

Tophat-2.0.10 not detecting Bowtie2-2.2.2

Dear all,

I just installed the newest version of Bowtie2 (2.2.0)

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

The version appears to be incompatible with Tophat 2.0.10 (it cannot find bowtie2, even if it is in the PATH).
The problem arises from the fact that the executable bowtie2-align disappeared, as two executables substituted it: bowtie2-align-l and bowtie2-align-s

The Tophat problem can be fixed by putting in the path a link to bowtie2-align-l named bowtie2-align

My question is: what are the two versions -l and -s? The difference is not documented anywhere, but it's present also in the bowtie2-build executables.

I am using Tophat-2.0.10 and Bowtie2-2.2.2. Inspite of giving paths, tophat2 is unable to detect Bowtie2. Is it because "bowtie2-align" is not there?
If so, can anyone of you suggest which version of Bowtie2 is compatible with tophat-2.0.10 ? Similarly which version of Bowtie is compatible with tophat-2.0.10.
Thank you

[giorgifm]

The Tophat compatibility problem can be fixed by putting in the path a link to bowtie2-align-l named bowtie2-align

ln -s bowtie2-align-l bowtie2-align

[dpryan]

I really wouldn't recommend linking the large-genome specific version of the script to the generic version unless you ONLY use large (i.e. >~4 gigabases) genomes and don't have any regular indices that you'd like to keep around. I wouldn't be surprised if the next release supports 64bit bowtie2 indices.

@genome1: Just upgrade to tophat 2.0.11, the version you're using is known to not work with the version of bowtie you have.

[genome1]

Thank you giorgifm and dpryan.
@dpryan: It is working.