I am looking for some help in setting the 'redundancy threshold' parameter that is to be specified while running SICER for calling peaks from histone data. The protein of interest here is a high mobility group nucleosome binding protein (HMGN1) which is predicted to have broad histone-like peaks.
As I do not want to remove duplicate reads from the input BED file, what do I specify for the 'redundancy threshold' on the command line. I am not able to leave it blank, as SICER expects something in that field.
I will appreciate any help or pointer in setting this parameter.
Thanks
As I do not want to remove duplicate reads from the input BED file, what do I specify for the 'redundancy threshold' on the command line. I am not able to leave it blank, as SICER expects something in that field.
I will appreciate any help or pointer in setting this parameter.
Thanks
Comment