Tool for detecting valleys in Chip-seq like data?
1
2
Entering edit mode
18 months ago
kxk302 ▴ 20

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

NGS Chip-seq • 1.2k views
ADD COMMENT
4
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
18 months ago
Thomas ▴ 20

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1651 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