Log Ratios of normalized tag count, greater or lower than 0

Question

[Bioradical]

I recently read a paper that used the following as a definition I am hoping to mimic "When H3K4me3 and H3K4me1 peaks overlapped, the regions were classified either promoters or enhancers if the log ratios of H3K4me3 and H3K4me1 normalized tag count was, respectively, greater or lower than 0".

Does anyone know how someone could do this using existing software? Maybe something like HOMER? Any ideas on how this was done?

Answer 1

[backfish]

Bit late but I used HOMER makeTagDirectory to create the Tags. Use makeUCSCfile to convert the directory to bedGraph format and if needed bedGraphToBigWig to create bigwig files.

Hope that helps anyway.