Understanding File Formats in Bioinformatics: ChIP-Seq files - BigWig (Wiggle) and BED/bigBed

Video Description

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. I hope you find this video helpful! Leave your thoughts in the comment section below! ▸ Types of high throughput data: https://youtu.be/wlY7vDdRfyo ▸ FASTA/FASTQ format: https://youtu.be/xYEre9DtIqA ▸ SAM/BAM file format: https://youtu.be/vh6l9aPFUgU ▸ Useful links: - https://www.encodeproject.org/data-standards/chip-seq/ - https://www.nature.com/articles/nprot.2011.420 - https://www.sciencedirect.com/science/article/pii/S1046202320300591 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 Like the videos I create? Show your support and encouragement by buying me a coffee: https://www.buymeacoffee.com/bioinformagic To get in touch: Website: https://bioinformagician.org/ Github: https://github.com/kpatel427 Email: [email protected] #bioinformagician #bioinformatics #chipseq #epigenomics #epigenome #atacseq #singler #10x #alleles #bam #vcf #gvcf #gatk #haplotype #alleles #variantcalling #geneticvariants #mutations #gff3 #gff #gtf #sam #bam #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs