How to curate ChIP-seq data, then normalize the depth?

Question

[Omar Mohamed]

I am an absolute beginner, and I am not sure if this question is legit, so I appreciate any comments.

I want to use ChIP-seq data for HeLa cells. I usually see the studies loaded multiple tracks of different histone modification or transcription factors of interest. My idea is that I want to combine all of them in tracks and analyze them for the functionally, states....etc.

So, I have few questions regarding the curation of all of these related to both biology and analysis:

How can compare in peaks and generate bed files that are consistent across different studies? I am not sure If any study would explicitly mention the depth sequencing, but I think this has something to do with the fastq file length!

Update: Here is the workflow I want to follow and I don't know if this is correct or not: 1. Search GEO for HeLa ChIP-seq and RNA-seq around certain gene. My selection will be INDEPENDENT of the study and depth, just the interesting data around the gene of interest. 2. Depending on the data, I have to reach to the point of bigwig and/or bed files so I can visulize the readings as tracks. 3. Visually (and hopfully statistcally), compare between the expression and different transcription factor and epigenetic modification presence or absence

I hope this clarify what I am trying to do.

Thank you!

Answer 1

[ATpoint]

Hello Omar Mohamed, any question from beginners is legit, that is what this community is for, so don't worry.

I think you need some kind of a beginner's tutorial to get familiar with the concepts of analysis.

These tutorials from the Harvard Chan Bioinformatics Core (HBC) are quite nice and provide lots of example code, see:

https://hbctraining.github.io/Intro-to-ChIPseq/schedule/2-day.html

Maybe see whether you can first work yourself through it and then edit your question to provide more details / a more specific question.

Some users also added quite a nice lits of resources here in this post which you should definitely check out, see:

ChIP-seq analysis: Tutorial for Beginners

[Omar Mohamed]

Thank you for your reply. I have been going throught the tutorials for sometime and now I know the basics of ChIP-seq.

The thing is that I now want to apply for a question of interest, and all the tutorial follow a similar approch of getting few ChIP-seq and RNA-seq from the same tissue (and same design I guess) to withdrew a conclusion.

To put my question more consicelly, I updated my question above with the procedure I want to apply answer my queston.