Tool for detecting valleys in Chip-seq like data?

Question

[kxk302]

Hello,

We would like to know about the tools used in detecting valleys in Chip-seq like data. Can the tools that detect peaks also detect valleys? Or, are there specific tools for valley detection?

Best,
-Kaivan

[Trivas]

How do you distinguish valleys from lack of signal/sequencing depth?

[Darked89]

Also: regions which can not be mapped using reads of length X.

[ATpoint]

I know of https://academic.oup.com/nar/article/44/9/4037/2462443 but never used it. Don't ask me whether reliable or not. For which analysis do you need that?

[kxk302]

Thank you all. I'll check the scipy tool and the paper.

Answer 1

[Thomas]

If you are comfortable with python, scipy has a find_peaks function you can use. This could be pretty easily adapted to your situation by multiplying your signal value by -1 to flip the data signal, then finding the peaks of the new signal.