Does anyone know/would be willing to give me a guide on how to do ChIP-Seq data analysis?

Question

[orchard4]

Hello everyone!

I'm not sure if this is the right place to post but I'm a PhD student who is completely new to bioinformatics and I have a lot of ChIP-Seq data to analyse. Unfortunately I'm pretty much on my own with this as my institution does not have a bioinformatician. Does anyone have a guide on what I need to do to analyse this or would be willing to provide me with a guide on how to analyse this? I'm really stuck and not sure where to begin.

Thank you!

[dsull]

I'd recommend looking at the methods section of published papers. Many good papers will present reproducible code or in-depth description of pipelines on how to reproduce their ChIP-Seq analysis.

Answer 1

[ATpoint]

Check the Bioconductor package csaw and previous threads on that matter to get a background. What is the question you aim to answer? Are you familiar with R? If not then the Galaxy platform might be a good place to start. https://usegalaxy.org/

[GenoMax]

https://usegalaxy.eu/ if original poster wants something close to home.

Answer 2

[antonioggsousa]

You may want to start by checking this tutorial on Galaxy: https://galaxyproject.org/tutorials/chip/