How to analysis 4c seq 3c seq data
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3.1 years ago
woongjaej ▴ 20

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!

3c seq 4c seq alignment • 1.1k views
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Entering edit mode
15 days ago
kalavattam ▴ 50

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).

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