StatQuest: A gentle introduction to RNA-seq

RNA-seq may sound mysterious, but it's not. Here's go over the main ideas behind how it's done and how the data is analyzed.
NOTE: If you want to learn about ChIP-seq, check out the StatQuest: • StatQuest: A gentle in...
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#statquest #rnaseq

[@statquest]

Support StatQuest by buying my book The StatQuest Illustrated Guide to Machine Learning or a Study Guide or Merch!!! statquest.org/statquest-store/

[@Nefglarien]

I can't believe it. I was actually crying and panicking when I clicked on the video because of all that stress caused by "I don't know, I don't understand" thoughts. And your intro just killed me XD

[@statquest]

Bam! :)

[@kristenapostol6288]

Me too!! I was breaking down internally from exam stress, then i watched the intro and it was like a breath of fresh air :,,,,)

[@alexanderpalm6407]

I've learned more from this 18-min long video, than my whole course in transcriptomics. You are so good at explaining these complex processes. Thank you!

[@statquest]

Hooray! :)

[@Pongant]

I know the feeling. Transcriptomics is so complex that most people, including those working in the field, seem to get "Betriebsblind" and unable to explain what they are actually doing. Josh Starmer is awesome, I just whish we had instructors like that in every research facility.

[@grace.florejost4611]

@@statquest same for me, I've understood this concept really easily thanks to you ( better than what I've understood in a 2h genetic engineering class )

[@himalayanplanespotter2021]

Hey Josh, I just started doing my RNA sequencing and your video was very useful for me to get the basic idea behind the RNA sequencing. I spent hours and hours reading papers and didn't understand a thing about it. I really appreciate what you have done. I think your channel will play a big role in my research. Hats off your efforts in coming up with useful informative videos like this.

[@statquest]

Awesome! That's great news. Since I made that video, I updated my PCA video to be easier to understand, so if you're interested in that, check out: kzbin.info/www/bejne/fJjEnI2ta7Bkh7M

[@Biomeducated]

@Highlander Yeti same for me! Just found out we're going to do RNAseq, immediately went on KZbin search instead of the classical science databases, came out here! I was already looking into (often expensive) courses, but it is all online! This is the future of learning. I should have had stuff like this 12 years ago to study Biomedical Sciences. That's why I'm on a mission helping future/current Biomeds and life scientists discover channels like this. Already BIG thanks from my part, StatQuest! I've yet to check out the rest of your stuff, but I WILL!

[@chasecolin22]

First you got me through my statistics course. Then you pulled me through my machine learning courses. Now, you will save me in my graduate genetics lab. Thank you so much Josh.

[@statquest]

No way! That’s totally crazy. Good luck with your lab! :)

[@Grillpander]

8:48 Two semesters of Bioinformatics and all I wanted was the sequence "GATTACA" to appear on any one slide during a lecture. Thanks, StatQuest for making my wish finally come true!

[@statquest]

Yes!!!! :)

[@bryanl1732]

thank you for making this video so accessible by having captions for everything

[@je6874]

This is honestly amazing... the best explanation on KZbin for RNA-seq!!

[@alexyang3086]

This is the clearest explanation in this sequencing videos. Usually explanation of such technology is hard, but they did a great job.

[@statquest]

Wow, thanks!

[@charlottel9717]

This technique finally makes sense! Thank you so much, this really helped a lot. Very clearly explained and easy to follow.

[@MrChaluliss]

Call this a 'gentle introduction' if you want. It is really just a high level overview of the process. Such presentations are important to building students mental models of any subject, and honestly are frequently overlooked in many subjects in my experience. Great stuff.

[@statquest]

Thanks!

[@paulristeca701]

So the "+" symbol used to be a section where individuals could ad more info about their sequence. This is back when we had far smaller output. Since then, data has grown so much that we have developed tools to go through the data more efficiently. In the end, the "+" is simply an artifact from the early days of these files.

[@matteobarca1050]

I'm not so sure about that, I think it was like that at the origin of this method, but in the new type of document layout, the + symbol could stand for "+ strand", which is often more investigated than the "- strand" of the double helix. I could be wrong, for sure, but I remeber like that

[@trannusaran6164]

These are great, I’ve been inundating myself with media about genomics and bioinformatics, but a lot of the specific techniques and terminology were still going over my head. Thanks for the thorough, but no-nonsense explanations!

[@taysaraujocamilo2313]

Hey! I'm Brazilian, and I've been learning English and molecular bioinformatics. I'm grateful for this video. Thanks a lot, your pronunciation is easy to understand and you have good didactics too.

[@statquest]

Muito obrigado! :)

[@maribelyazdanifar8823]

Thank you for the clear explanations. This was the first time I learned how the machine reads the bases by taking pictures from the top with single base annealing intervals. It was very informative. I am heading to watch your other videos. Many thanks!

[@statquest]

Glad it was helpful!

[@MrsPacmaaan]

I'm writing my bachelor's thesis about RNA-seq and usage of this method in the viruses life cycle, u helped me a lot in understanding this. Thank you!

[@torlarsen2212]

I LOVE gentle intros

[@statquest]

double bam! :)

[@stevensilz-carson1793]

Thank you for this. My current molecular bio professor recommedned we see it before our first class, and it was well worth the 18 minutes!

[@statquest]

That's awesome! I'm glad you liked the video. :)

[@elfa4231]

Fantastic video. This is the kind of gentle explanation students (including myself) need. Many thanks from Sweden!

[@statquest]

Glad you enjoyed it!

[@alexeileliavski732]

Very impressed how you explain pseudo-alignment! So clear and so concise! Amazing!!

[@statquest]

I'm working on a new video that will do a whole analysis pipeline from start to finish and will include pseudo-alignment.

[@Silvver]

This is actually one of the easiest-to-understand videos I have ever watched about this subject. Thank you for making it so that I can actually understand the information being taught!

[@statquest]

Glad it was helpful!

[@daedrmr2dae]

@@statquest same comment! patiently explained without assuming we're all experts, written text of what you are saying verbally, simple, pedagogical, and systematic. It's great teaching, and so happy it's free!

[@statquest]

@@daedrmr2dae Thank you!

[@simafarokhnejad5882]

This is one of the best videos for explaining RNA-seq. You are fantastic. Thank you very much.

[@statquest]

Thank you! :)

[@steveskalski5363]

Simple, concise, and straight forward. Well worth the 18 minutes.

[@statquest]

Thank you! :)

[@leileicui5803]

Bro, super love the various title songs you used for each videos, that attract me to the statistic world! Thank you!

[@statquest]

Hooray!!! :)

[@yi4763]

The intro song gets me every time ha. But honestly thanks for breaking down the concepts for a newbie like me, keep up the good work

[@leyiwang3863]

The intro song really fits me lol. I'm literally crying and watching StatQuest right now.

[@statquest]

Bam!

[@reggie1021]

Oh wow. Thanks for the explanation! I didn't really understand this concept until now. I've watched this video 3 times now because it is so comprehensive. Thanks a lot.

[@statquest]

Glad it was helpful!

[@emfazz96]

1:27 I love that you did this

[@asmaakterbhuiyan_shanu3951]

I am seeing this video in December 2021 and I can't thank you enough for this incredible concept clearing video of RNA-seq. Very Concise and subtle explanation, Besides your ENGLISH is really understandable for other language speakers. I am gonna check another playlist too.

[@statquest]

Thank you!

[@janebond3263]

You stop my worring , stress and anxiety! thank you God and bless Josh Starmer!

[@statquest]

Thank you very much! :)

[@leipingzeng3018]

Excellent course! Thank you for making these stuff so clear! It's much easier to understand!

[@statquest]

Hooray! I'm glad the video was helpful. :)

[@reflections86]

Hey JOSH…First thanks for making such great videos over the years. I see that you even left your job as a professor and have devoted full time to make this stuff since 2017. Appreciate it as it is difficult to break your comfort zone. One thing I would say after reading books on mastery is that all elite masters have this skill to explain a tough concept in 2 minutes and they can drag the same concept for hours and hours. From thousands of comments on your videos, majority says you make things extremely simple which is a validation of mastery. The second aspect of elite masters are after working for about a decade and mastering a field then they bring innovation or a new thing (a new concept, theory, a formula, anything that was never explained). I’m sure this would be that phase and stat quest is part of that, and I hope many things would come along with your creativity which you have exploited to make this elite content. There are masters but very few have this skill to make things simpler. Many people might comment that you have mastery or talent in statistics or in music but I can say without any doubt that your talent lies is making complex things easier (the medium could either be through a video or through a book don’t matter), but that’s your core talent which you have used. So I wish you keep using this rare talent and bring more contribution to all the humans. I will certainly support statquest by purchasing the guides and encourage all who have benefited from this content. Thanks again and lastly is there any email if I could send you a message or share something of value. Will appreciate it.

[@statquest]

Wow! Thank you very much!!! BAM! :)

[@bojanristivojevic3396]

Thank you so much for this video. It is a great starting point for me, and I have a feeling that I'll be coming back to your channel. Keep up the great work! :)

[@mcatprep7053]

best explanation for this on youtube.... Thanks man. You're the best.

[@renataialchina8887]

Thank you so much for this very gentle intro to RNA-seq. It helped me with my defense!

[@statquest]

Hooray!!! Congratulations on your defense! I hope it went well. :)

[@sanjanatule]

This is an amazing video! I have learnt a lot. We would like to see more videos on bioinformatics.

[@brunoguerra4650]

Amazing content ! Easy to understand and complete as possible for YT! Keep it up! Cheers !

[@andromeda3780]

Normally I get bored very quickly from explanation but hey this didn't feel like 18 mins at all :D Very useful content and you explain the ideas in pretty well organized way. Thank you that was really helpful ✔

[@statquest]

Thank you very much! :)

[@liubajc6130]

I loved this explanation!!!. It is the most didactic I have seen of all. Congratulations and many thanks. It was very useful. I really appreciate what you have done.

[@statquest]

Thank you so much!!! :)

[@helenarg520]

I think it's great how there's an effort to speak and pronounce clearly; It really helps when you're not a native English speaker!

[@statquest]

Thanks!

[@cedrichill7499]

Thanks for this tutorial. It's much better than others I've viewed.

[@statquest]

Thanks! :)

[@sa19h1j]

Josh Starmer I love you, man. I have been spending hours reading and have only added stress and headaches after Thank you so much

[@statquest]

Happy to help!

[@jeswang8532]

This is so clear! I'm so happy I checked this. Thank you!

[@statquest]

You’re welcome! :)

[@stylutionnet]

This is an incredibly brilliant playlist. Thank you sp much for your videos!

[@statquest]

Glad you like them!

[@dianalauralabastida9166]

This is really well-explained! You got a suscriber! Hope you continue making videos

[@statquest]

Thank you very much! :)

[@marystroka7]

It's an amazing video! Thank you for this Josh!

[@LintonF1]

Clear, concise, well done! Loved it!

[@statquest]

Thank you very much! :)

[@fifi7244]

im so glad I found ur channel to potentially save my course

[@statquest]

Hooray and good luck! :)

[@tiberium87]

This is utterly fantastic, thanks a lot for making these!

[@30tomthomas]

this is the clearest explanation on the internet about rna seq, everywhere else makes it sounds like gobbledygook

[@statquest]

Hooray! I'm glad you like my video. :)

[@user-cv9pv6nn9l]

Thank you for this video! It help me a lot, I didn't find anywhere a clear explanation of this content.

[@statquest]

Glad it was helpful!

[@patriciamunyadzwe1023]

Thank you so much for the video, I have been having headache to grasp the RNA seq concept, now I am set for transcriptomics module.

[@statquest]

bam! :)

[@yiannisconstantinou4834]

Super helpful and informative, thank you!! You are amazing at explaining things!

[@statquest]

:)

[@MrErPeeeG]

According to the "+" in fastQ, I have heard once, that in this line it used to be a repeat of the sequence name without "@" at the begining, to ensure that quality regards to the sequence above, but to lower file weight it has been switched to the "+". That's what I have heard, but it would be worth to approve somehow this information, I have no sources to do that.

[@sweboulund]

I was taught in my course in metagenome and microbiome analysis, that the + line exists so you can put comments there! Never seen one with comments though.

[@oliverslay6687]

MrErPeeeg is correct; but also it signals the end of the sequence lines. FastQ spec: @ +[] A requirement is that the following '+' is optional, but if it appears right after '+', it should be identical to the following '@'. maq.sourceforge.net/fastq.shtml

[@RamakrishnanRS]

The reason is that FASTQ is a combination of FASTA and QUAL files. Each of those has identifier followed by data. FASTA has sequence, QUAL has quality scores. interleaving these two pieces of information (2 lines from each file "zippered in") gives us 4 lines where 2 of the lines are identical. Later on, when machines got smarter, the third line became obsolete (and expensive space-wise) but is retained in a stunted form for backward compatibility.

[@saramalik5440]

Too many ads

[@nunitchagucci3047]

Thank you! This is the best video I have ever seen! ❤️

[@statquest]

Awesome!

[@yimingzhang1251]

Really helpful video, and extremely easy to understand for beginners, many thanks!

[@statquest]

Glad it was helpful!

[@Thisispow]

Hey, really good video! This was very educational, straight to the point and very much coherent. Thanks

[@statquest]

Thank you!

[@preeti97rox]

Your channel is a blessing i might clear an interview after watching all this xD

[@statquest]

Good luck! Let me know how it goes. :)

[@Charlottes_WorldWideWeb]

My God Lord this was heaven sent. Any you guys are hilarious! I don't think it's "excessive self promotion" at all, I'm going to watch your PCA one right now!

[@briansalkas349]

Less than half way through, already learned more than an entire online course!

[@statquest]

bam!

[@NM-tx7zm]

Your videos help me immensely! Thank you!

[@statquest]

Thanks!

[@munaalhammadi4237]

"+" sign in raw data indicates the forward strand. If paired-end sequencing was performed there will be files with"+" or "-" signs that indicate forward or reverse strands, respectively.

[@statquest]

Thanks!

[@sdsa007]

this makes sense… i think its easy for the machine to figure out in the beginning since probably the oligo adaptors, which bind to the flow cell floor, are probably colour-coded for forward and reverse adaptors, and the adaptors themselves, are also probably colour coded, and the camera can pick up on this at the start, which means the algorithm can interpret forward and reverse strand locations and write it to the file.

[@hikadani]

i love you. cozy stat vids. this is good for the soul

[@statquest]

Thanks! :)

[@janebond3263]

You are totally amaizing! Thank you so so much for so complete explanations . Some details are diff to find or figure out.

[@statquest]

Thank you! :)

[@JJ-zq5pp]

thanks for so many details and explanations! really helpful!!!

[@statquest]

Hooray! :)

[@Sveccha93]

I finally understand like ten things. Thank you!

[@statquest]

Hooray! :)

[@wissenistmacht6685]

This is such a good video. I felt lost until now. Thank you

[@statquest]

bam! :)

[@norestforthescientist1154]

As a scientist with no previous experience in big data (who will need to be tuned in for my new research position), all I can say is THANK YOU.

[@statquest]

Thanks!

[@dist321]

Thank you very much for your videos! They are indeed clearly explained.

[@statquest]

You’re welcome!

[@CWunderA]

Thanks Josh, great overview!!

[@statquest]

Thanks!

[@Mightyriderable]

I really like your Intros!

[@giovannaamaral9019]

I just loved it! You made it so simple! Thank u so much!

[@statquest]

Thank you! :)

[@annie0tan]

Hey. I'm a clinician trying to do a basic sciences post doc. I haven't touched my biology notebooks in 10 years... and your Video makes it look... like I could maybe, one day, perhaps... UNDERSTAND transcriptomics. (Also makes me feel like an idiot, but in a gentle and kind manner). Thanks

[@statquest]

Good luck! :)

[@luissoto4525]

Jaaaaaah I love it , please continue doing more videos like this.

[@dewisukma5297]

Thank you for sharing, it is very useful to increase my knowledge of RNAseq

[@statquest]

Glad it was helpful!

[@sahintakci1220]

amazing video, the best of all that I see

[@sarahnardeli]

Thank you for the videos Josh! Even for experts users it is a great didactic content! ;)

[@statquest]

You're welcome! I'm glad to hear my video is so helpful. :)

[@urjaswitayadav3188]

Wow, super good intro. Thanks!

[@abinaya276]

you are literally saving my entire life rn

[@statquest]

Happy to help! :)

[@suhanguo2316]

Love the song! Also, thank you for explaining the fragments part. I didn't know that I don't fully understand the rationale behind fragmentation until you explained it. It's an important side note to understand RNA-seq.

[@statquest]

Glad you liked it!

[@agentgunnso]

Yay! thank so much for this video!!! you are excellent!!!

[@statquest]

Glad you liked it!!

[@ahsenkonac7992]

Super helpful and clear! Thanks!

[@statquest]

Glad it was helpful!

[@zahraghorbanali98]

So Useful!!! Thanks for the explanation :)

[@statquest]

Thank you!

[@ethanjavan]

thank you so much for the awesome simple explaining

[@statquest]

Thanks!

[@awhb5412]

Thank you, good easy to understand explanation

[@statquest]

Thanks! :)

[@mingweisun1590]

Fantastic explanation! Thank you!

[@statquest]

Thanks!

[@luisfqo1]

This is amazing, thank for the video!

[@statquest]

Thanks! :)

[@papridas5542]

Nice explanation. Thank you sir!

[@statquest]

Thanks!

[@oscarmunoz2269]

good explanation and graphics keep up the good work

[@statquest]

Thank you! :)

[@nanobioinformatician9324]

excellent, very helpful. Thanks a CPM for sharing :)

[@tabishhussain3660]

I loved the video...Very well explained...Can you also make a video about the analysis of raw RNA-Seq data, that is getting from raw reads to FC, FDR and p values for each gene...

[@gabrielerosso9612]

Hello congratulations for the video. Very clear and well explained. Thank you! I'd like to have some clarifications: 1) minute 9:14 when you say "the genome fragments that matched the reads fragments will determine a location (chromosome and position) in the genome" basically means that for reads aligned/mapped we know their position with respect to the reference genome, or are you referring to something else? 2) minute 9:29 - I don't understand why breaking read sequences into small fragments. In the example (9:45) you say that the first fragment will not match beacuse of the A mismatch, but also with some mismatches reads can map on the reference genome. So why make fragments is a better choice. Moreover fragments too small improve multimapping, not good for gene expression profiling. Could you clarify my misunderstanding? 3) Finally i ask you with what program have you created these images. Thanks!

[@ericgathirwa8454]

Great description. Thank you. Additional information/description about the sequence may be put in the third line that starts with the +

[@statquest]

Thank you very much! :)

[@rrrprogram8667]

Ya I even can watch Statquest when I am bored ... Great video

[@statquest]

Nice!!! :)

[@msumode4493]

THank you so much. Best explainer ever.

[@statquest]

Hooray! :)

[@nobuhlendlovu9961]

Thank you! This was very helpful👏

[@statquest]

Glad it was helpful!

[@dhkwnr97]

Thank you. It`s a really good video.

[@aditipatel5916]

how grateful i am to the universe to find this 20hours before my interview

[@statquest]

Good luck! :)

[@aleksandrat.5058]

I am also revising before my interview :D

[@statquest]

@@aleksandrat.5058 good luck!

[@kiranraj1553]

This is the best video ever. Thanks a lot!!!

[@statquest]

Glad you liked it!

[@mohammedmonzurmorshed2896]

concise and priceless..thanks so much

[@statquest]

Thank you! :)