Question: Compare ChIP-seq data from various experiments
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gravatar for bharath.mh24
22 months ago by
bharath.mh240 wrote:

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

ADD COMMENTlink written 22 months ago by bharath.mh240
1

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...

ADD REPLYlink written 22 months ago by John12k
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