create a RC matrix with narrowPeak data

Question

[chavezfigueredo.alejandra]

Hi everyone, I'm new in this field; actually I'm a data science master student and I'm doing my master project about a kind of clusterization of MCF7 cells and since my project is not too big I'm working just with the peak files from encode. Well, for this project one of my first step is to build a read count matrix with the peak data, I was reading a lot about this and all the different kind of analysis that I can make it confuse me a lot, so, I'm looking for an advice or recommendation to build this matrix.

Thanks a lot.

Alejandra

[Ram]

This is a question, not a forum discussion topic. I'm making the necessary changes, but please be more careful in the future.

[ATpoint]

What exactly made you confused? From all the approaches that you read about, which seemed most promising to you and where did you get stuck? Based on my personal experience, for the long term you learn so much more from finding out the solutions for these basic analysis steps yourself, rather than getting a ready-to-use script from a more experienced user. Please give some details on where you got stuck, then we try to put you back on track.

Answer 1

[Rory Stark]

The DiffBind package in Bioconductor creates a read count matrix from peak calls and aligned reads.