HOMER mergePeaks --matrix output?

Question

[morovatunc]

Dear all Hi,

I would like to ask you something related with mergePeaks — matrix option.

In this option it creates a count matrix. However, I found something interesting.

I ran the following command and it created a matrix. Why the matrix is not symmetrical? Because when we compare two files shouldn’t it give the same number of overlapping peaks independent of the order? How should I interpret this ?

As far as I know, this option compares two individual at a time. It gives a number of matching peaks between two samples. Could you illuminate me in terms of the interpretation of this output?

Thank you for your help,

Best,

Tunc.

Part of the matrix.

      H2azPk        H3k04me1
H2azPk  0       23545
HH3k04me1   23508   0

My command was as below.

mergePeaks -d 500 Helas3H2azPk.broadPeak.bed Helas3H3k04me1StdPk.broadPeak.bed Helas3H3k09me3Pk.broadPeak.bed Helas3H3k27acStdPk.broadPeak.bed Helas3H3k27me3StdPk.broadPeak.bed Helas3H3k36me3StdPk.broadPeak.bed Helas3H3k4me2StdPk.broadPeak.bed Helas3H3k4me3StdPk.broadPeak.bed Helas3H3k79me2StdPk.broadPeak.bed Helas3H3k9acStdPk.broadPeak.bed Helas3H4k20me1StdPk.broadPeak.bed -matrix hela