When we trim 3' ends of reads of a Input sample to improve their 'sequence quality', should we also trim by the same number of bases in 3' ends in corresponding ChIP samples even if sequence quality in ChIP samples is good? I mean, do ChIP and Input reads always have to be the same size?
My own quick perspective: all samples should be pre-processed in the exact same way. It may not change the overall 'feel' of the results, but you will face more criticism if you pre-process them differently without any major justification. If one sample was horrendously poor quality, then you could justify special treatment, but otherwise no.