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Has this issue been resolved? Any updates? I'm dealing the exact same errors/error logs as described above.
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Unfortunately no. Your only option is to use TopHat 2.0.9 on OS X, unless you want to try compiling from source (not simple).Comment
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Ok. Thank you. I'll continue with v.2.0.9 then. I'm still waiting for a response from the developers after I reported the issue. Once I get an update I will post it here.Comment
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Weird. After I replaced Tophat's 2.0.12 version with the 2.0.9 version it doesn't find bowtie anymore. Even though it's in the PATH. I tried with --bowtie1 and --bowtie2. Bowtie2 is present as I can access it from the command line.
What's the catch?
[2014-08-27 09:09:09] Beginning TopHat run (v2.0.9)
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[2014-08-27 09:09:09] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.Comment
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You may need a corresponding older version of bowtie to go with TopHat 2.0.9. Try v.2.1.0.Comment
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Thank's. That worked.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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