This is a test version of Biostars. For the public version, visit https://www.biostars.org.
peaks in IGV

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
• 4,520 views • link
written by yueli7 yueli7

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)

• 0 views • link
written by Ram Ram

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

• 0 views • link
written by Ram Ram

2 answers

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

Hello, WouterDeCoster, RamRS,

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

enter image description here

• 0 views • link
written by yueli7 yueli7

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.

• 0 views • link
written by ATpoint ATpoint

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

• 0 views • link
updated by GenoMax GenoMax • written by yueli7 yueli7

Log in to answer this question.

More posts like this
  • enriched genes PPI network
    written by yueli7 yueli7
    Hello, I want to make a figure just like below Figure 1. I went to string database and made a search: https://string-db.org/cgi/input?sessionId=bHX2BS9VeUGo&input_page_show_search=on. The result just …
  • Frequency of the gene expression in Seurat
    written by yueli7 yueli7
    Hello, I can go through the Seurat all the code from here: https://satijalab.org/seurat/archive/v3.0/visualization_vignette.html. My question is: Is that possible that I can get the frequency …
  • phred score per base sequence quality
    written by yueli7 yueli7
    Hello, I have RNA sequencing data. After running FastQc, it comes out bad result. Do I need to fix it? Thanks in advance for any …
  • how I can download both of the two files from ebi
    written by yueli7 yueli7
    Hello, I want to download the files: SRR8611991_4_R1_001.fastq and SRR8611991_4_R2_001.fastq from https://www.ebi.ac.uk/ena/data/view/SRR8611991. But I only can download one SRR8611991.fastq file. How can I download both …
  • with *.aligned.sorted.bam.featureCounts but without *.ex.featureCounts or *.in.featureCounts
    written by yueli7 yueli7
    Hello, Anyone, I played with zUMIs-zUMIs.0.0.6/zUMIs-master.sh -f barcoderead_HEK.1mio.fq.gz -r cDNAread_HEK.1mio.fq.gz -n 1 -g /home/li/reference/hg38_chr22 -a /home/li/reference/hg38_chr22/GRCh38.84.chr22.gtf -c 1-6 -m 7-16 -l 50 -o /home/li/li01 In …
  • question ablout seurat figure PC_contribution
    written by yueli7 yueli7
    Hello, Anyone now what is the mean of following figure? I know it is the PC_1, what is the number in x-axis? It comes from …
  • Build signal track
    written by yueli7 yueli7
    Hello, I followed the post https://github.com/taoliu/MACS/wiki/Build-Signal-Track "Fix the bedGraph and convert them to bigWig files And you will have these bigwig files: flag1_FE_01.bw and flag1_logLR.bw" …
  • chip-seq visualize tool IGV
    written by yueli7 yueli7
    Hello, I tried to use IGV to visualize my chip-seq peak file. Why it is so strange? The peak is not smooth? Thanks in advance …
  • How to use MACS2 to do peak calling
    written by mikysyc2016 mikysyc2016
    Hi all, I see two website to introduce MACS. Now i have a bam file which one I should use? I attach them below: 1. …
  • MACS2 with multiple replicates
    written by ariel.balter ariel.balter
    When you use macs2 with [multiple replicates](https://github.com/taoliu/MACS/wiki/Build-Signal-Track#run-macs2-combining-replicates) is it just pooling the replicates or doing something more sophisticated?