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Question: Query related to generating plots from HOMER output
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gravatar for pinky_pinkpinky
4.3 years ago by
pinky_pinkpinky • 50
India
pinky_pinkpinky • 50 wrote:

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
chip-seq homer • 1.6k views
ADD COMMENT • link •
modified 4.3 years ago by bede.portz • 470 • written 4.3 years ago by pinky_pinkpinky • 50

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

ADD REPLY • link written 4.3 years ago by geek_y ♦ 9.4k
0
gravatar for bede.portz
4.3 years ago by
bede.portz • 470
United States
bede.portz • 470 wrote:

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
ADD COMMENT • link written 4.3 years ago by bede.portz • 470

Thanks for your suggestion.

ADD REPLY • link written 4.3 years ago by pinky_pinkpinky • 50
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