How to improve signal to noise ratio in sequencing samples?

Question

[Maurice]

Hi everyone!

I'm dealing with NGS data derived from CUT&TAG experiments and I'm quite new to the field. I ended up with very noisy IGV profiles and sample coming from my antibody of interest looks like my IgG one. I used MACS2 for peak calling against my IgG but few peaks are visible.

How can I reduce background noise? Are there any available tools to get rid of the background signal and to improve the signal to noise ratio between my sample of interest and IgG?

Thank in advance to everyone that will help me!!!

Answer 1

[ATpoint]

No, data quality is a property that comes from the lab procedure. There is no in silico magic to rescue a poor ChIP. You can (in the lab) try to optimize the protocol, for example optimizing antibody concentrations or try different antibodies. If there is no good antibody for your protein you might consider making a cell line with a fusion tag, for example HA-tag or some sort of tag that can be biotinylated and then ChIP that, hoping the tag does not notably alter protein function.