This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Meta-Analysis chip-seq data

Hello all.

Can I do Meta-Analysis by CHIP-seq data with different antibodies??????

Thanks a lot

meta_analysis chip-seq next-gen
• 1,686 views • link
updated by Rory Stark Rory Stark • written by Brice222 • Brice222

What do you define as a "meta-analysis"?

• 0 views • link
written by John John

i want to (meta-analysis) find Important peak in samples

• 0 views • link
written by Brice222 • Brice222

No one is gonna answer your question correctly if you use a vague term. Meta literally means anything.

• 0 views • link
written by datascientist28 datascientist28

i want getting, the important common peaks in different experiments chip-seq

• 0 views • link
written by Brice222 • Brice222

You need to add more information. Describe your experiment. What does "important" mean?

• 0 views • link
written by WouterDeCoster WouterDeCoster

Hello Brice222!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

• 0 views • link
written by WouterDeCoster WouterDeCoster

1 answer

What's "important" depends on the biological quesiton.

If your experiment is properly designed with replicates, you can do a differential analysis to find the peaks that are significantly differentially bound between conditions (eg different antibodies). The DiffBind package in R/Bioconductor does this and has a step-by-step tutorial. You can also do simple overlaps (venn diagrams) to find peaks in common or peaks unique to a condition, but you can't get confidence statistics for this.

-R

• 0 views • link
written by Rory Stark Rory Stark

Log in to answer this question.

More posts like this