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