Question: peaks in IGV
0
gravatar for yueli7
6 weeks ago by
yueli740
China
yueli740 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 • 245 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by yueli740

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 6 weeks ago by RamRS23k

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

ADD REPLYlink written 6 weeks ago by RamRS23k
2
gravatar for WouterDeCoster
6 weeks ago by
Belgium
WouterDeCoster40k wrote:

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

ADD COMMENTlink written 6 weeks ago by WouterDeCoster40k

Hello, WouterDeCoster, RamRS,

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

enter image description here

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by yueli740
2
gravatar for ATpoint
6 weeks ago by
ATpoint21k
Germany
ATpoint21k 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 6 weeks ago • written 6 weeks ago by ATpoint21k

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 6 weeks ago by genomax70k • written 6 weeks ago by yueli740
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