I have a TF chip-seq study with two types of replicates:
2 Flag+TF samples, each with a corresponding IP control (Type A)
2 Flag- samples, each with a corresponding IP control (Type B)
I am attaching stats (% uniquely aligned, non-aligned, duplicates, initial number of paired peaks, estimated fragment size, number of positive and negative peaks) about each treatment-control pair:
As you can see, the type B treatment-control pairs have a large number of negative peaks (9511 for the treatment-control pair in the first table row and 2009 for the treatment-control pair in the third row). I would not have expected any peaks - neither positive nor negative as no TF factor was added to any of these samples. There are some other anomalies (e.g. high percentage of non-aligned reads in the IP controls) which may or may not be related to this phenomenon. I checked some of the non-aligned reads but they don't seem to produce any BLAST hits so they may be some sort of technical artifacts. I don't know how to proceed with these samples - shall I throw them out? Any advice is most welcome.