peaks in IGV

Question

[yueli7]

Hello,

I used https://github.com/taoliu/MACS/wiki/Build-Signal-Track to build signal track, and tried to use IGV to see my peaks.

Why my peaks so strange? When I zoomed in, there is no peaks.

Thanks in advance for any help!

Best,

Yue LI

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

[Ram]

Are you seeing something that's not expected? What is the difference between the expected output and the actual output?

Answer 1

[WouterDeCoster]

You are looking at the entire genome in your screenshot. Select a locus of interest.

[yueli7]

Hello, WouterDeCoster, RamRS,

Thank you so much for all of your's kindly response!

Answer 2

[ATpoint]

You have to scale the y-axis. Right-click on the track and select auto-scale. Please read tools and documentations of the tools you use. Also, as Wouter says, zoom in as you are looking at the entire genome.

[yueli7]

Hello, ATpoint,

Thank you so much for your kindly response!

Right click, change track height 100, set data range, set data range 0,0,6, and marker log scale.

Right click, autoscale, log scale.

Thanks again

Best,

Yue