View Single Post
Old 08-21-2013, 06:43 AM   #9
Junior Member
Location: Freiburg, Germany

Join Date: Apr 2013
Posts: 3

Originally Posted by Lizex View Post
Hi SDiehl
Did you get a solution for your problem you had regarding Tophat not opening gzip. I think I have a similar problem. I have compiled and installed Tophat2. When running tophat on the test_data, I got this error:
test_data $ tophat2 -r 20 test_ref reads_1.fq reads_2.fq
Error: cannot find compression program gzip

It says it cannot find the compression program gzip. Any idea or suggestion what I should do?

Thanks in advance

In my case gzip was not the problem. For some strange reason it turned out the be the reference. After I redid the reference everything worked fine again.

As GenoMax already said, most likely you need to install gzip or add it to your path, such that tophat can find it.
SDiehl is offline   Reply With Quote