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Question: Cuffdiff
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gravatar for Irene Bassano
6.4 years ago by
Irene Bassano • 90
United Kingdom
Irene Bassano • 90 wrote:
Hi, just few questions about cuffdiff if anyone can answer: 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files 2.what to use as input: cufflinks, cuffcompare or cuffmerge? Thanks a lot!
rna-seq cuffmerge cufflinks • 829 views
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modified 6.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.4 years ago by Irene Bassano • 90
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gravatar for Jennifer Hillman Jackson
6.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Irene, Change the tool form for the option "Perform replicate analysis:" to be "Yes" (the default is "No"). Use two conditions (Groups). GTF output from any of these may be appropriate. Please see the tutorial on Galaxy main at: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise FAQ: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq And the "Common uses" protocols on the Cufflinks web site plus their new paper (also linked at this site, from side bar, as "Protocol"): http://cufflinks.cbcb.umd.edu/tutorial.html Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k
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