Compare ChIP-seq data from various experiments

Question

[bharath.mh24]

Hello All, I am interested to know if there is any way I could compare and visualize (IGV or UCSC genome browser) normalised ChIP seq data from various different ChIP-seq experiments(Different cell lines). I would like to have all the datasets' peaks on the same viewing scale(Data Range). Do I have to normalize in a specific manner? Would be extremely grateful for any ideas provided. Thank You

[John]

You can certainly view the data in IGV as a bunch of tracks, however there are packages specifically designed to compare ChIP-Seq data such as deeptools2 (which, full disclosure, is produced in the same institute that I work). However, you still have to be very careful when doing this sort of analysis. Typically the batch effect in ChIP-Seq is high. Data from different labs is rarely comparable. In fact data from the same lab over different years/sequencing technology is rarely comparable. These sorts of experiments should really be done "for purpose", and not as publicly usable reference dataset. Which ironically is my job to produce...