Question: peaks in IGV
0
gravatar for yueli7
12 months ago by
yueli7140
China
yueli7140 wrote:

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

https://ibb.co/mJqgBqk

chip-seq • 543 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by yueli7140

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)

ADD REPLYlink written 12 months ago by RamRS27k

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

ADD REPLYlink written 12 months ago by RamRS27k
2
gravatar for WouterDeCoster
12 months ago by
Belgium
WouterDeCoster44k wrote:

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

ADD COMMENTlink written 12 months ago by WouterDeCoster44k

Hello, WouterDeCoster, RamRS,

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

enter image description here

ADD REPLYlink modified 12 months ago • written 12 months ago by yueli7140
2
gravatar for ATpoint
12 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by ATpoint36k

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

picture03

ADD REPLYlink modified 12 months ago by genomax85k • written 12 months ago by yueli7140
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