ChIP-seq data analysis

Question

[Silas]

How to find peak-associated genes regulated in ChIP-seq data? Thanks!

[Matthias Zepper]

At which stage of the analysis are you? Which protein have you immunoprecipitated?

Without you providing more information, it will be hard to help, since e.g. a transcription factor that binds to enhancers will be more complex to assign to genes than say a H3K36me3 ChIP-seq. But out of the blue: If you are at the start, have a look at the nf-core ChIPSeq pipeline or Homers NGS tutorial. Use e.g. Homer to annotate genes to peaks.

[Silas]

I have a ChIP-seq data report from a company.I would like to find peak-associated genes regulated in ChIP-seq data. I have many files like fastqr; mapping; peak calling; peak annotation; diff; findMotifs... and the backup. But I do not know how to find... I have checked the peak calling and peak annotation. Thank you in advance for your help, I've been struggling for a few months. The protein is RGL2

[Matthias Zepper]

If a company has provided you with that output, I would primarily suggest contacting their customer support for help.

But if you have fastqs; mapping; peak calling; peak annotation; diff you should have all that you need. Usually, the peak annotation should be the file where the peaks are annotated with features such as genes or enhancers. Since you said you looked there already: How does this file look like? I suppose it is a .csv or .tsv file that you can open with Excel. Doesn't it contain some annotation columns?

May I ask in addition, if you are working with human data or one of the common model organisms, or is it from an organism with very little annotation available?

[Silas]

I have a ChIP-seq data report from a company.I would like to find peak-associated genes regulated in ChIP-seq data. I have many files like fastqr; mapping; peak calling; peak annotation; diff; findMotifs... and the backup. But I do not know how to find... I have checked the peak calling and peak annotation. Thank you in advance for your help, I've been struggling for a few months. The protein is RGL2 and I wanna get the peak-associated genes regulated.

Answer 1

[MolGeek]

If you have a peak list, you can use chipseeker to annotate the peaks to genes.