Hello,<br><br>When I attempt to run cufflinks based on .sam output from bowtie I get an error:<br><br>An error occurred running this job: <i>cufflinks v1.0.1<br>cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -b /galaxy/data/hg19/sam_index/hg19.fa<br>
Error running cufflinks. [Errno 2] No such file or directory: &#39;transcripts.gtf&#39;<br><br></i>What can I do to get around this problem and run cufflinks?<br><br>My workflow is on <a href="http://main.g2.bx.psu.edu">http://main.g2.bx.psu.edu</a> and can be found here (I ran it using a .fastq file):<br>
<br><a id="item-url" href="http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-uploaded-file" target="_top">http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-uploaded-file</a><br><br>
Thanks in advance for your help!<br><br>-David<br><br><br>************************************************<br><br><div>David Robinson<br>
Graduate Student<br>Lewis-Sigler Institute for Integrative Genomics<br>
Carl Icahn Laboratory<br>Princeton University<br>
646-620-6630<br>
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