Question: Chipseq peaks HOMER annotation results
0
gravatar for Mike
16 months ago by
Mike880
UK
Mike880 wrote:

Hi,

I am using HOMER for peak annotation, I used macs2 peaks as a input for HOMER, and I got HOMER output with 19 column, 6th column is Peak Score. What is meaning of peak score & How this calculate?

this is my HOMER command:

perl ~/homer/bin/annotatePeaks.pl chip_peaks.bed hg19   >homer_out.txt

Thanks in advance.

chip-seq homer • 940 views
ADD COMMENTlink modified 24 days ago by EagleEye4.9k • written 16 months ago by Mike880

Which organism you have used in your analysis ?

ADD REPLYlink written 15 months ago by ####160

human cell line data

ADD REPLYlink written 15 months ago by Mike880
0
gravatar for EagleEye
24 days ago by
EagleEye4.9k
Sweden
EagleEye4.9k wrote:
  • Homer annotatePeaks does not give you peaks score, it just annotate your peaks to known genomic regions.

  • Homer findPeaks will give you peak score which is, Peak score (position adjusted reads from initial peak region - reads per position may be limited). http://homer.ucsd.edu/homer/ngs/peaks.html

  • In your case if you are using MACS output as input to Homer annotatePeaks, the peak score you see is calculated from MACS (not Homer). Peaks scores are usually log10 transformed pvalues or FDR (depending on the preference, check manual of the tool). https://github.com/taoliu/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands

ADD COMMENTlink modified 24 days ago • written 24 days ago by EagleEye4.9k
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