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:
• Types of High Throughp...
▸ FASTA/FASTQ format:
• Understanding Bioinfor...
▸ SAM/BAM file format:
• Understanding Bioinfor...
▸ Useful links:
- www.encodeproject.org/data-st...
- www.nature.com/articles/nprot...
- 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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To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: [e-mail]
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[@shantanujain3732]

This was a great explanation. Thank you :)

[@varshatripathi9857]

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

[@abdelrahmanmahany133]

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

[@lailanhass1988]

Thanks!

[@shajibdey6451]

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.

[@mervanbayraktar5269]

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

[@user-rk4tl7xx2i]

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

[@florianm5639]

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:)

[@Bioinformagician]

A common approach for dealing with repetitive regions is to mask or filter out these regions. ENCODE provides a list of such blacklisted regions. In your case, it seems the outcome is favorable. You should not expect to see a significant peak in your repetitive region (in most cases). Repetitive regions may appear enriched by looking at the number of reads mapping to that region, hence it is important that the ChIP-Seq profile is compared to a matched input control to determine its significance.

[@florianm5639]

@@Bioinformagician Actually, that would not be favorable, as I am working on such a region. But maybe the method then is just not suited? In any case. Thanks for the reply!

[@Bioinformagician]

Thank you for clarifying it. Sorry, I misunderstood your query initially. Determining significant peaks in repetitive regions can be challenging. One way you could improve the detection of peaks in these regions, is by lowering the p/q value threshold while calling peaks (for programs like MACS), however be wary of lots of noise and false positive peaks that you will be getting in your results. Another rudimentary way that I can think to determine significant peak enrichment, is to calculate the number of reads mapping to these regions in your sample and matched normal and calculating fold change. The fold change would give you a good indication for enrichment in that region. Lastly, I recommend referring to a published study that have studied chromatin modifications and transcription factor binding to rDNA as there could be orthogonal methods/assays which I am not aware of, that you can use to add confidence to your findings by the methods mentioned above.

[@florianm5639]

@@Bioinformagician Sounds like a good place to start! Thank you!

[@Po0pypoopy]

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

[@localsofindia1457]

may i know what u are doing now?

[@Po0pypoopy]

@@localsofindia1457 nothing….i have given up on life

[@Po0pypoopy]

@@localsofindia1457 nothing since I gave up on life