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,
Part of the matrix.
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