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.
I hope you find this video helpful! Leave your thoughts in the comment section below!

▸ Types of high throughput data:

▸ FASTA/FASTQ format:

▸ SAM/BAM file format:

▸ Useful links:

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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[shantanujain]

This was a great explanation. Thank you :)

[varshatripathi]

Plz make a vedio of Pathway enrichment analysis through Cluster profiler package...

[ihassanabidi]

I have an Excel file containing genomic coordinates with columns for chromosome, start, stop, and strand (example below):

Chr, Start, Stop, Strand

chr18, 46097960, 46098231, -

chr19, 46089854, 46089890, +

Using this data, I need to identify and extract genomic features such as promoters, 5' UTRs, 3' UTRs, intergenic regions, exonic regions, and intronic regions. How can I accomplish this?

[mervanbayraktar]

Thank you so much for the work that you’re doing, can you please make video about genome wide association study and genetic diversity and population structure best regards

[RaphaëlGondran]

Hi. very infomative video.
Could you do a video about Methylation NGS data treatment if you are familiar with it ?
Thanks a lot !

[abdelrahmanmahany]

Thanks for the great effort. Can you recommend the sequence to watch your playlists so that it would be in the right order? Thanks again

[shajibdey]

Hi. Informative video indeed.
If I have some hypothetical proteins of a bacteria, will I be able to get it's gene ID?
please let me know. Thanks in advance.

[florianm]

Great video! Very clarifying! I have a further question. How does one deal with repetitive regions such as the rDNA locus? In my dataset I see the highest read count at the rDNA but for some reason it is not called as a significant peak. Do you have any idea on how to deal with this? Thanks:)

[Popypoopy]

I’m not sure if you have made a video on this already but :

Can you make a video about how to get into bioinformatics ?

I quit my job as a wet lab assistant from a research lab 2.5 years ago and haven’t done anything related to biology since then because I was very upset with the income and lack of learning opportunities, I have zero letters of recommendations now because I quit when my boss and colleague didn’t want me to because they really needed me even though I was upset. I currently just have a bachelors.

I’m having a very hard time figuring out how to get into this field with no letters of recommendations

Would trying to make a personal project be enough? Should I join clinical research trials and learn some biostatistics?

I feel like nobody would want me if I can’t get any letters of recommendation 😢

Lost and need help….thanks