Understanding File Formats in Bioinformatics: ChIP-Seq files - BigWig (Wiggle) and BED/bigBed
In this comprehensive guide on ChIP-seq file formats video, I delve into details of ChIP-sequencing, experimental and computational workflow and types of controls used. Further, I briefly discuss Irreproducible Discovery Rate (IDR) and discuss some commonly used ENCODE terminologies. Lastly, I go over the details of .bigwig, .bigBed and BED (BED6+4 and BED6+3) files and discuss various ways one can visualize ChIP-Seq data. Whether you are a seasoned researcher or a newcomer to the field, this video will provide you with the knowledge you need to navigate ChIP-Seq data effectively.
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▸ Types of high throughput data:
• Types of High Throughput Data in Bioi...
▸ FASTA/FASTQ format:
• Understanding Bioinformatics File For...
▸ SAM/BAM file format:
• Understanding Bioinformatics File For...
▸ Useful links:
https://www.encodeproject.org/data-st...
https://www.nature.com/articles/nprot...
https://www.sciencedirect.com/science...
Chapters:
0:00 Intro
0:42 What is ChIP-Seq?
3:01 ChIP-Seq experimental workflow
4:16 ChIP-Seq computational pipeline
6:12 Downstream analysis using ChIP-Seq data
7:04 Controls in ChIP-Seq experiments
8:59 Types of ChIP-Seq peaks: How do narrow peaks, broad peaks and mixed peaks look like?
9:51 What is Irreproducible Discovery Rate (IDR)?
11:14 ENCODE terminologies
12:59 ChIP-Seq file formats
14:36 narrowPeak vs broadPeak file specifications
18:26 Ways to visualizing ChIP-Seq data
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Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
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