Question: peaks in IGV
0
gravatar for yueli7
20 months ago by
yueli7190
China
yueli7190 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 • 1.0k views
ADD COMMENTlink modified 20 months ago • written 20 months ago by yueli7190

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 20 months ago by Ram32k

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

ADD REPLYlink written 20 months ago by Ram32k
2
gravatar for WouterDeCoster
20 months ago by
Belgium
WouterDeCoster45k wrote:

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

ADD COMMENTlink written 20 months ago by WouterDeCoster45k

Hello, WouterDeCoster, RamRS,

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

enter image description here

ADD REPLYlink modified 20 months ago • written 20 months ago by yueli7190
2
gravatar for ATpoint
20 months ago by
ATpoint46k
ATpoint46k 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 20 months ago • written 20 months ago by ATpoint46k

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 20 months ago by GenoMax96k • written 20 months ago by yueli7190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1757 users visited in the last hour
_