I'm comparing between MEDIPS and QSEA for methylation analysis of pulldown sequencing. I've split my genome into 200bp windows, and then added the data from my bam files.
My question is between the two, MEDIPs adds a read into each window that it lies within, whereas QSEA only puts the read into the window where the read centre of mass lies. This gives a big difference between the two in terms of normalised counts, particularly for windows are split around the centre of a peak.
I'm interested in the rationale between the two design decisions, and potential ramifications downstream.