What is sequencing depth? | Bioinformatics 101

In this video I explain a term frequently used with sequencing i.e. depth associated with coverage (or depth of coverage, sequencing depth or read depth). In addition to discussing what these terms mean, I talk about what is the recommended coverage for different NGS data, how to visualize coverage and how to calculate coverage and coverage metrics from BAM files using samtools.
I hope you find this video helpful! Leave your thoughts in the comment section below!
Chapters:
0:00 Intro
0:32 What is coverage?
1:23 Depth of coverage (or sequencing depth)
1:49 Breadth of coverage
2:32 How to calculate coverage? (Lander/Waterman equation)
4:15 Recommended sequence coverage for NGS data
5:42 Visualizing coverage
6:17 Calculate coverage and coverage metrics
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[@crazychill6263]

I just wish I had someone like you to ask all my questions
I´m completely lost in bioinformatics and it´s sooo hard to find someone to explain it to you in plain English or even find basic information 😐

[@shobhitashah1929]

So far the best channel for genomics beginners!

[@aamirmalik7740]

Fantastic explanation of the concept -- please also continue with the lecture series you started on RNA Seq pipeline from scratch previously. Many Thanks

[@user-lx3qr6zl7l]

your videos are extremely helpful! thank you so much ! i will follow your channels and watch every of your videos, please continue your update!

[@tushardhyani3931]

Thank you for this video !!

[@sonalvishwakarma30]

Thanks! Please make more tutorials✨

[@nasreenbano523]

Too good explanation.
What will be the best recommended coverage for hi-C sequencing??

[@shrijasrao9464]

what will the sequencing depth for wheat GBS ?

[@davidtupatron]

Great video! You literally clarify everything! I have a question, what woukd be the recommended depth for assessment of SNPs in a amplicon sequence? 🤔 and also, does the error rate play a role in getting the depth?
I hope you could answer my question! Thank youuuu

[@Harshraj19988]

I am trying to calculate the sequencing depth and coverage of WGBS data. I have bam files. So for samtools, input file is bam file or sorted bam file?

[@javiersanjuan296]

How can I calculate coverage for amplicon sequencing if I have multiple amplicons of different sizes pooled together? Should I use an average size for all the amplicons?

[@slendrmusic]

best bioinformatic channel

[@zlj8435]

Thanks a lot!

[@animatedbiologywitharpan]

Great explanation

[@saurabhthakar]

Now I am assured that I am watching high-quality content because you are here.

[@mongekantorovich3555]

Thank you!

[@hubijohn7451]

awesome!

[@emanuelavilla4733]

Great video! They are very useful, even to refresh the topic! I have a question, which may be a stupid one, but how do we decide the sequencing depth for single-cell RNA and ATAC? There are any recommendations?

[@Bioinformagician]

Excellent question! I do not think there is a straightforward formula or criteria to answer that question. I think there are a lot of factors involved like (and not limited to) heterogeneity of population cells (whether one is trying to identify rare cells populations), whether certain genes are expressed at high level in the condition or population you are investigating (if one is trying to investigate if a certain gene is expressed in certain cell population), sample type library, platform and cost.
Of course there are recommended sequencing depths for single-cell RNA and ATAC libraries, but ultimately depth has to be adjusted based on the application and budgeting constraints.
I am linking some articles which may be of interest -
genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0467-4
www.nature.com/articles/nbt.3039#:~:text=Large%20sample%20sizes%20impose%20a,reads%20per%20cell%20may%20suffice.
www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression/documentation/steps/sequencing/sequencing-requirements-for-single-cell-multiome-atac-plus-gene-expression
kb.10xgenomics.com/hc/en-us/articles/115002022743-What-is-the-recommended-sequencing-depth-for-Single-Cell-3-and-5-Gene-Expression-libraries-

[@juanete69]

Why is it important the direction of the read?

[@anamikapandey4769]

great lecture😍, please make a video on ChiP SEQ data analysis.....it will be more helpful for us

[@Bioinformagician]

That is definitely in the pipeline. Please stay tuned :)

[@anamikapandey4769]

@@Bioinformagician thank you💜

[@ch00p]

At 4:11 why is the coverage for the single bp region 5X? LG/N = 8(5)/1=40X. Is this just an exception for single nucleotide regions?

[@Bioinformagician]

It's an exception for single nucleotide regions.

[@AyrodsGamgam]

it's 1(5)/1=5X, because it's only one nt

[@sanjaisrao484]

Thanks

[@Fabiano1012]

👏👏👏👏

[@himanshusaxena387]

It's a fine video, but it sounds more bookish. Should try to express more simply (language particlarly) and graphically.