Compare ChIP-seq data from various experiments
0
0
Entering edit mode
5.1 years ago

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

ChIP-Seq Normalize Visualisation • 2.2k views
ADD COMMENT
1
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2210 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6