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Question: Rna Seq Analysis
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gravatar for puvan001@umn.edu
7.6 years ago by
puvan001@umn.edu • 80
puvan001@umn.edu • 80 wrote:
I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the steps up to cufflinks and I did not have any problems. Thanks for the RNA seq tutorial. My questions are 1. How do I know the number of reads mapped against the reference genome used after Top Hat mapping 2. I am aware that Cuffdiff is used to find the differences in expression. How do I combine replicates (3) of different treatments ? SP
rna-seq cufflinks • 876 views
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modified 7.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.6 years ago by puvan001@umn.edu • 80
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gravatar for Jennifer Hillman Jackson
7.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, Please try: "NGS: SAM Tools -> flagstat provides simple stats on BAM files" Set the "NGS: RNA Analysis -> Cuffdiff" form so that the second choice, "Perform replicate analysis:" is "Yes". The ability to add/define groups from your history will pop up when the form modifies in response to this selection. Best wishes for your research, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD COMMENT • link written 7.6 years ago by Jennifer Hillman Jackson ♦ 25k
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