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Question: DESeq2 results versus by eye comparison in IGV
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Entering edit mode
4 months ago
kathryn.eckartt • 20

Naive question but is it common for the fold change in gene expression for a locus to appear greater by eye in IGV than in the fold change calculated by DESeq2?

For example, the log2FC of geneA is -1.667704322

IGV view of geneA

These tracks are group autoscaled.

Thank you in advance!

RNA-Seq IGV DESeq2 • 66 views
ADD COMMENT • link 4 months ago kathryn.eckartt • 20 • updated 4 months ago swbarnes2 5.7k
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Entering edit mode
4 months ago
swbarnes2 5.7k
United States

IGV likely is not normalized, and DESeq is.

ADD COMMENT • link 4 months ago swbarnes2 5.7k

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