Tophat 1.3 beta version

[mwang]

Hi,

Did anybody here try to use the lastest tophat 1.3.0 version? I downloaded their Linux x86_64 binary file and installed it in my 64bit redhat Linux box. When I tested the installation using the test_data based on their manual, I got an error message "Permission denied" when tophoat "Checking for Bowtie". I am sure Bowtie is in my PATH.

I tried to download their source codes, compiled, and installed by following their installation guide, I got the same error message when running the test_data.

After several frustrating trials, I downloaded and installed their x86_64 Linux binary file of the old tophat 1.2.0 from their website. I did NOT get the error message any more when I run the test_data and my own illumina RNA-seq data.

If anybody here successfully installed and used the last version 1.3.0 in 64bit linux machine, I would greatly appreciate if you could share your solution.

[lshen]

when you type bowtie , will it run?

One simple fix maybe to put bowtie binary to under the same folder as tophat.

chmod 755 your_path_to/bowtie

[mwang]

Hi Ishen,

Thank you very much.

I used bowtie alone for my sequence analysis. It worked great.

I put bowtie and tophat binary file in one fold as you suggested. It works now.

Wish the tophat team could fix the problem in the future.