Dear Dr Stark and Dr Brown,
Thank you very much for providing a great computational tool to the scientific community for the differential binding analysis of data from ChIP-seq experiments. I have two questions:
1) question regarding the correlation plots generated by Diffbind using peak occupancy data (peak scores) from the peak caller output files: The MACS2 output files for a given sample only contains q values for the peaks that were called in that sample. If–log10q values are provided to Diffbind as peak scores in the peak set input files for the samples then what score does diffbind assign to a given sample for a peak in cases where the peak was called in other samples but not in that sample.
2) question regarding counts and control samples: Are log transformed read counts used for the differential binding analysis? If log transformed counts are used then how does Diffbind normalize ChIP read counts with respect to control read counts- does it subtract log transformed control read counts from log transformed chip read counts or does it first subtract actual control read counts from actual chip read counts and then log transform the value obtained? In other words are the chip counts normalized to a fold value with respect to the control read counts or do the normalized counts represent the arithmetic difference between chip and control read counts?
Thanks
Chintan Parekh
You can get the peak scores from MACS2 NAME_peaks.narrowPeak file..
# I write it as an answer by mistake..