Chipseq peaks HOMER annotation results

Question

[Mike]

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.

[####]

Which organism you have used in your analysis ?

[Mike]

human cell line data

Answer 1

[EagleEye]

• 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