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Question: Cuffdiff Values Different For Same Sample
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gravatar for i b
6.1 years ago by
i b • 330
i b • 330 wrote:
Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values as expressed in the output (isoform differential expression). When I ran it again, using a different treated sample, but SAME UNTREATED SAMPLE, the values assigned to the untreated are different. Why is this if values are calculated from a unique FPKM? This happend for other jobs where I have ran the same untreated vs other treated samples... Thanks a lot, ib
rna-seq cuffdiff • 1.4k views
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modified 6.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.1 years ago by i b • 330
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gravatar for Jennifer Hillman Jackson
6.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, Would you be able to share a history containing these data? Use "Options (gear icon) -> Share or Publish", generate the share link, then copy and paste that into a reply email sent to me directly. Please note the dataset #'s for the Cuffdiff runs that you are comparing and make sure that all inputs are undeleted. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
6.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, Thank you for sharing your history. The difference in FPKM values can be explained by the use of the -N option ("Perform quartile normalization: Yes"). Set this to "No" to avoid the variable per-run normalization. This has also been discussed at seqanswers.com: http://seqanswers.com/forums/showthread.php?t=4606 Hopefully this helps! Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k
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