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Old 08-21-2013, 07:43 AM   #9
SDiehl
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Location: Freiburg, Germany

Join Date: Apr 2013
Posts: 3
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Quote:
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

Lizex
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.
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