I want to create a heatmap for chip-seq data by Homer program http://homer.salk.edu/homer/ngs/quantification.html
the command is like this:
annotatePeaks.pl <peak file> <genome> -size <#> -hist <#> -ghist -d <tag directory 1> [tag directory2] ... > <output matrix file>
My problem is the peak file. it requires a bed file with a column of peak strand.
BED files should have at minimum 6 columns (separated by TABs, additional columns will be ignored)
- Column1: chromosome
- Column2: starting position
- Column3: ending position
- Column4: Unique Peak ID
- Column5: not used
- Column6: Strand (+/- or 0/1, where 0="+", 1="-")
But I used MACS to call the peaks, where the algorithm is combined two peaks from both directions into one. So there is no such info as strands (If my understanding is correct).
Can anyone tell me how to solve this issue? Can I just assume all the peaks are from either one of the strands?