Chip Seq controls
Hello All,
I am presently working with breast cancer chip seq data housed in EBI for a variety of transcription factors. When I run MACS2 peak caller without control , I find some random peaks where are no where close to gene promoters.I was looking for control files for the experiments, but till now did not succeed.Any suggestions. Thanks in advance.
• 1,573 views
•
link
updated
by
Ian
•
written
by
wani.nisar •
•
written
by
wani.nisar •
1 answer
You could use blacklists from ENCODE/modENCODE to remove false peaks that overlap blacklisted coordinates.
Have you checked GEO or ArrayExpress to find input for the tissue you are investigating.
Log in to answer this question.
More posts like this
-
Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
written by sk •
-
High Variability when Peak Calling with SEACR
written by hunter.a.ogg •
-
chip seq data visualization in UCSC genome browser/Chip base / cistrome browser
written by angajalaanusha •
-
How to compare different chipseq peak calling methods?
written by jesvinjoy35 •
-
Peak calling macs vs Homer
written by saurabh.j.pradhan •
-
Best databases for Chip-Seq
written by JS •
-
ENCODE ChIP-Seq Control Experiments
written by ghazalhaddad •
-
How can I increase the number of peaks using macs2 peak caller?
written by GK1610
-
ChIP-Seq Histone modification time span study
written by Sudhir Jadhao
-
Tweaking Findpeaks Output
written by darcangelo.elisa •
