Query related to generating plots from HOMER output

Question

[pinky_pinkpinky]

Dear Users,

I performed motif analysis for Chip-seq data using HOMER.

I want to generate a plot from HOMER output having Distance between binding sites (bp) in X-axis and

Number of binding sites in Y-axis. I am not able to interpret from HOMER motif results which data has to be considered for generating such plots.

Any suggestions.

Thanks

Abhi

[GouthamAtla]

Can you provide an example plot or few lines of data ?

Answer 1

[bede.portz]

AnnotatePeaks should be able to do this.

annotatePeaks peakfile1.bed genome -size # -hist # -noadj -d peakfile1.bed > output.txt

Here the first peak file will be the reference against which the second peak file will be plotted against.

-size # is the area around the first peak file about which you want to plot the second peak file. i.e. -size 500 would be +/-250 bp around the first peak file
-noadj option means you don't normalize the # of peaks or reads in either dataset, so the Y-axis should give you the number of peaks in each plot.
-hist# refers to the bin size

Check out the HOMER manual, under the "Histograms of Tag Directories" heading. This gives you instructions that I think will help you, straight from the author of the tool, rather than a novice, such as myself.

http://homer.salk.edu/homer/ngs/quantification.html

[pinky_pinkpinky]

Thanks for your suggestion.