Question: Cufflink Does Not Work!
6.4 years ago by
Jennifer Hillman Jackson ♦ 25k
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Di Nguyen, Without seeing your history, my initial guess is that the SAM output from the mapping runs need to be sorted before running Cufflinks. (Tophat, which is designed to map spliced RNA-seq data, sorts the SAM output as part of the data processing, but BWA and Bowtie do not). The workflow provided on this FAQ can be followed to sort SAM files for Cufflinks: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis- faq#faq2 If you continue to have problems, please submit a bug report (click on "green bug" icon from the error Cufflinks dataset as run on the main public Galaxy instance (http://usegalaxy.org), leave all inputs and the error dataset undeleted, note this email address in the comments if it differs from your Galaxy account email address (so that I can link the two issues together), and we can provide more feedback. http://wiki.g2.bx.psu.edu/Support#Error_from_tools Hopefully this helps, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
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