Question: DESeq2 results versus by eye comparison in IGV
0
gravatar for kathryn.eckartt
3 days ago by
kathryn.eckartt20 wrote:

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!

igv rna-seq deseq2 • 105 views
ADD COMMENTlink modified 2 days ago by shawn.w.foley710 • written 3 days ago by kathryn.eckartt20
4
gravatar for swbarnes2
3 days ago by
swbarnes25.8k
United States
swbarnes25.8k wrote:

IGV likely is not normalized, and DESeq is.

ADD COMMENTlink written 3 days ago by swbarnes25.8k
2
gravatar for shawn.w.foley
2 days ago by
shawn.w.foley710
USA
shawn.w.foley710 wrote:

As swbarnes2 said, the biggest question is going to be normalization. What exactly is in IGV? Are you just looking at counts? Have you normalized for sequencing depth? I see both tracks are on the same scale, but does that blue track actually go above 90? I'd also say that DESeq2 is reporting a 3-fold change, by eye I can't say that those tracks are greater than or less than 3-fold. It's also worth noting that whatever counting algorithm you're using (htseq, salmon, etc.) is summing the reads across the whole locus, there are some regions where you have more reads in the red plot, and other regions where there are more in the blue.

All this is meant to say that there's a lot more going on than what's easily detectable by eye. I'd look at that IGV track and say there's a noticeable difference in coverage, and it's going in the expected direction (I assume, I don't know what your samples are). If you don't see anything noticeable, or if the change is going in the wrong direction then I'd start being concerned and digging into the code. As it is, your data look good!

ADD COMMENTlink written 2 days ago by shawn.w.foley710
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