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Question: Cufflinks Error In Galaxy
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gravatar for 吳正華
7.5 years ago by
吳正華 • 60
吳正華 • 60 wrote:
Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis according to Jeremy's excellent tutorial http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise however, I encountered following error messages when I was trying to execute Cufflinks in galaxy.. Dataset generation errors Dataset 121: Cufflinks on data 92: gene expression Tool execution generated the following error message: Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' The tool produced the following additional output: cufflinks v1.0.3 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4 -b how should I solve this problem? Thanks in advance. Best Regards, John Wu
rna-seq cufflinks • 858 views
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modified 7.5 years ago by Jeremy Goecks • 2.2k • written 7.5 years ago by 吳正華 • 60
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gravatar for Jeremy Goecks
7.5 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
John, My best guess is that you are using bias correction but do not have the needed reference genome(s) for the builds that you want to use. See this page for instructions about setting up HTS tools; in particular, you'll need to set up the sam_fa_indices.loc file: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup Best, J.
ADD COMMENT • link written 7.5 years ago by Jeremy Goecks • 2.2k
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