Hello,

The problem is most likely with the SAM files and sorting. Please see:
"Why won't my SAM dataset work with Cufflinks?"
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2


Best,

Jen
Galaxy team

On 9/26/12 12:54 PM, Kenneth Auerbach wrote:
Hi,

I'm also getting these error when I run cuffmerge. It was run without a
reference so it shouldn't have anything to do with the reference. Can
you please tell me how to fix this?

Thank you.









--
Jennifer Jackson
http://galaxyproject.org
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