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!
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.