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Old 08-21-2013, 06:28 AM   #7
Location: Cape Town South Africa

Join Date: Feb 2011
Posts: 22
Default Tophat gzip program not found

Originally Posted by SDiehl View Post
Thanks for the reply JonB. I tried running tophat2 on two different powerful servers which both have much more than 8GB memory.
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

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