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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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
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