HOMER annotatePeak -ghist --- lose of peaks?

Question

[martinm]

Hi Everyone,

A question on losing sites when running HOMER´s annotatePeaks.pl with settings: -hist and –ghist :

I´m creating a neat heatmap from a previously generated peakfile, where I visualize binned reads from each site (as described here: http://homer.ucsd.edu/homer/ngs/quantification.html - Creating Heatmaps from High-throughput Sequencing data).

I´m using HOMER´s annotatePeaks.pl to create the data file. I´m binning a 3kb window into 50 bins with the following command:

annotatePeaks.pl MyPeaks.bed mm9 -hist 50 -ghist -size -1500,1500 -d MyTagDirectory.TD > BasisOfMyHeatmap.txt

Here´s the problem: MyPeaks.bed (original peakfile) contains circa 82000 sites. BasisOfMyHeatmap.txt (output file) contains circa 79000 sites. Why am I losing peaks in this analysis?

All the best

Martin