How to analysis 4c seq 3c seq data

Question

[woongjaej]

Hi, guys

I have 3c seq fastq raw data.

I searched how to analysis 3c seq data and got confused.

I think basic analysis pipeline of 3c seq is different from other sequencings, right?

For example, for other sequencing data, I first trim and QC the raw reads and get in to alignment with reference genome. But I found for 3c seq data somehow a bit different.

Could some one have experience in 3c 4c seq data analysis, give me the basic concept of 3c 4c seq analysis?? (ex. step1 trim, step2 align ....) And I found some packages for analysing 3c seq data saying virtual fragment libraries. What is virtual fragment library?

Any help will be very grateful for me....

Thank you guys!

Answer 1

[kalavattam]

To start, you can check this paper, "4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis," and relevant repos for computational processing and analyses (pipe4C and peak4C).