And when I tried running tophat alone like this:
tophat -r 20 test_ref reads_1.fq reads_2.fq
I get this error:
[2012-12-19 06:57:07] Beginning TopHat run (v2.0.7)
---
[2012-12-19 06:57:07] Checking for Bowtie
Bowtie version: 2.0.2.0
[2012-12-19 06:
This is the error I am getting while running Tophat. What's causing this? I
have the default hg19 index files.
Error in tophat:
[Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3)
---
[Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_ou
