How to use IGV (or any genome vis tool) show normalised ChIP-Seq peak intensity?
I have a question about IGV, I am quite new on ChIP-seq data.
- In analysis side, I use MACS2 for peak calling, MAnorm2 for normalisation. etc, the result looks good.
- In IGV side, I generated bigwig file from bam files from
bamCompare, then loaded these bigwig files for visaulisation.
If my understanding is correct, what IGV shows are not-normalised peak intensity.
Below are two genes I identified that should have higher peak intensity value in LT and NC phenotype, and low peak intensity in the middle lane (TC). However, the IGV plot does not seems in accord with my result.
XX.MeanValue represent the mean normalised peak average value on the gene body. I understand the plot in IGV is using different measurements (bigwig) as analysed peak intensity (normalised log2(count)), but I am expecting they show a similar trend.
| | AllCount| NC.MeanValue| TC.MeanValue| LT.MeanValue| |:-----------------------------|--------:|------------:|------------:|------------:| ... |chr1-BTNL10 | 24| 1.9539123| 1.1080244| 1.6104720| |chr10-VIM | 153| 0.8124961| 0.5232620| 0.8462570| ...
So my feeling is, I should try to converted normalised peak intensity into bed files, then use IGV to read these bed files, in this case, I should be able to ask IGV to show normalised peak intensity, as I right? Have anyone tried this?
• 63 views
Read more here: Source link