If you benefit from my tutorial and use the same strategy for data analysis, please CITE my RNA-Seq paper published in "Scientific Reports - Nature": www.nature.com/articles/s41598-017-16603-y And "PLOS ONE": journals.plos.org/plosone/article?id=10.1371/journal.pone.0194485 ●Chu, C.P., Hokamp, J.A., Cianciolo, R.E. et al. RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy. Sci Rep 7, 16776 (2017). ●Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, et al. (2018) Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLOS ONE 13(3): e0194485.
You prolly dont care but if you are bored like me atm then you can stream pretty much all of the new movies on Instaflixxer. I've been binge watching with my girlfriend recently xD
I am a Bioinformatics degree student from Malaysia and I have no experience on NGS and RNA-seq analysis but watching this video makes me want to learn more. Thank you so much for sharing your knowledge. This video is very helpful :)
Thank you for a great video Candice, I have just started an Honours Project which includes RNA-seq and I feel like this hour just saved me at least a weeks work!!
Thank you Candice for your nice introduction to RNA seq.. i was wondering what and how around a year.. but now I'm in a clear pathway....please continue...
What a great video! Aside from the well presented information, your tribute to your cat touches my inner emotions. As a soon to retire internal medicine physician, I am progressing in learning RNA-Seq technology in order to pursue my specific research interests. I appreciate your insights and applaud your kindness to learners and all creatures. Mark McCaulley, .MD, FACP
Thank you so much Candice! This is a very well structured lecture and I absolutely loved it and finally understood the whole analysis pipeline! You are definitely someone I look up to and I hope one day I could present my research as well as you did! Thank you!
41:41 Anyone know how to obtain the hgnc_symbol? I used cuffdiff which gave me XLOC gene IDs but I can't seem to find a way to effeciciently convert them to common gene names.
Thank you Candice! This has been very helpful. I just about to start an RNAseq experiment and its really great to see the workflow from start to finish.
Thank you for this clearcut guiding in the tremendous world of omics. Though, the last few minutes of your vid were perhaps the most valuable... Big hug, Candice!
This is a great video I learned a lot! thanks! and I am so sorry for your cat passing away to early. from one cat lover to another, I know the feeling too well, and send you my deepest condolences.
Thanks for the video! It was helpful to me. I also shared it on the r/bioinformatics subreddit as I think others might also benefit from it. The ressources you provide are great, both in quantity and in quality.
Hi Candice, firstly, thank you for your video. I'm watching in 2021, but maybe like you I'm stuck in 2016 as my dog and best friend passed away about a month and a half before your cat (1996.01.09-2016.08.14), so I sympathize deeply. Life will never be the same, but I'm trying to throw myself into research to see what I can learn about what it all means...
Very useful Candice, thank you for the video and useful resources -definitely helpful - ooo my pug died a while back, I know how you feel...stay blessed!
Thank you for this informative session. It was very helpful for me. I wanted to ask if you have resources available, can I get all.deseq2.R script. I am doing some work with plants around 30 samples.
You are great helpful. It's really interesting that I've already read your post on Biostar 2 weeks before. I thought this guy is really help. Wooh, see you again here in youtube.
Thank you very much for this video. I benefited greatly from this and will definitely try to use the same approach for my project. I'm so sorry you lost your cat; I lost mine 2 weeks ago and I know how it fells
Thanks for the upload. Shame about the sound at times. Can you elaborate on why at 20:09 you chose HISAT2 (instead of STAR) for alignment and HTseq (instead of StringTie) for quantifying expression levels and DESeq2 (instead of Ballgown) for differential expression? Thanks!
Hey Tommy, sorry for the late reply. I have been working on finishing my PhD and getting a new job lately. I wasn't very into STAR at the time I was doing the analysis, but now I am aware that more and more people are using STAR for alignment. As for the differential analysis, I briefly mentioned the reason in my paper (see the first comment). Michael Love, the creator of DESeq2, is on Bioconductor ALL THE TIME. He almost immediately answered all my questions. Alternatively, you can use EdgeR, but DESeq2 is more conservative so you get less false postive genes.
Thank you so much for this talk. It really helped me figure out what tools to explore using for my reserach. And I’m so sorry that your cat passed away.
Im bioinformatic noob i wanna know @30:12. Is where index located? Do i need to create these files before runnign hisat2 right? And right now in manual it is . Is it the same? Thank you in advance
Hi,Thank you so much Candice! This is a very well structured lecture and I absolutely loved it, I am beginner and I need more help to understand RN sequence analysis.
Hey Candice I’m wondering if your answer to the question about why RNA-seq is used instead of Protein profiling, you mentioned the current technology isn’t sensitive enough to profile all the proteins. But I think RNA- seq has the same problem. Are you able to sequence all the RNA molecules in present in that condition?
Thanks for the video. I need to use a published E. coli RNA seq data to see the particular region of interest. This is to find out the RNA reads in a region of interest. Do you have any video tutorial to do this alignment with the genome and visualize this data?
Thanks for the article. So helpful! Another question; Can a missing biological replicate affect the transcripts abundance and differential expression pattern of genes? How a missing replicate can be dealt during the differential expression analysis?
Thanks a lot for this nice tutorial. Do you have any suggestions for the fungal RNA Seq analysis or I can still follow the protocol mentioned in the tutorial.
Hi, Thank you so much for the informative presentation. I have few questions. Is it possible to calculate t & p values without replicates? Why some FastQc report gives boxplots without boxes and only lines?
This was really great to help me understand the entire process. I really enjoyed it. Is there a way for me to do this without having access to these packages like hisat2 and HTseq? I don't think I can download them on my computer and even if I did the flies that will be analyzed by this are too big to download. what are my option if I want to do an independent project?
[ RE: read trimming ] Trimming low quality reads isn't as necessary as it once was. Most state-of-the-art aligners (including HISAT2) take quality scores into account and will "soft clip" as needed.
![Seungmin "그렇게, 천천히, 우리(As we are)" | [Stray Kids : SKZ-PLAYER]](http://i.ytimg.com/vi/kAzmhLHePqU/mqdefault.jpg)
If you benefit from my tutorial and use the same strategy for data analysis, please CITE my RNA-Seq paper published in "Scientific Reports - Nature": www.nature.com/articles/s41598-017-16603-y
And "PLOS ONE": journals.plos.org/plosone/article?id=10.1371/journal.pone.0194485
●Chu, C.P., Hokamp, J.A., Cianciolo, R.E. et al. RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy. Sci Rep 7, 16776 (2017).
●Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, et al. (2018) Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLOS ONE 13(3): e0194485.
very useful!Thank you!
You prolly dont care but if you are bored like me atm then you can stream pretty much all of the new movies on Instaflixxer. I've been binge watching with my girlfriend recently xD
@Gerald Joaquin definitely, been using InstaFlixxer for since december myself :D
Candice chu Great Lecture
تاغتس172تدشءى. كشذ1مضشش
This is the BEST video I had seen!!! Finally someone did the step-by-step in an approachable manner. Thanks Candice. Great job!
Even after years, i found this video is the best for explaining RNA-Seq analysis from top-bottom. Thanks a lot @Candice Chu.
I am a Bioinformatics degree student from Malaysia and I have no experience on NGS and RNA-seq analysis but watching this video makes me want to learn more. Thank you so much for sharing your knowledge. This video is very helpful :)
The best video on RNA seq analysis, also with loads of resources. Thank you.
看到一半突然看到繁體中文的google介面才驚覺你是台灣人!
謝謝您的講解 祝您在美國一切順利!
希望有天也能到達您的高度~
This is one of the best tutorials I've seen on any subject, thank you so much for this!
Thank you for a great video Candice, I have just started an Honours Project which includes RNA-seq and I feel like this hour just saved me at least a weeks work!!
Super useful! You know exactly what a beginner needs to know. And that's really interesting you introduce the websites. It keeps us updated. Thanks
Thank you Candice for your nice introduction to RNA seq.. i was wondering what and how around a year.. but now I'm in a clear pathway....please continue...
What a great video! Aside from the well presented information, your tribute to your cat touches my inner emotions. As a soon to retire internal medicine physician, I am progressing in learning RNA-Seq technology in order to pursue my specific research interests. I appreciate your insights and applaud your kindness to learners and all creatures.
Mark McCaulley, .MD, FACP
Thank you so much for this video! It opened my mind to know how to analyze my rna-seq data. It was really perfect! Congrats.
Excellent talk. I highly appreciate the good work. Currently working on rnaseq work.
Thank you so much Candice! This is a very well structured lecture and I absolutely loved it and finally understood the whole analysis pipeline! You are definitely someone I look up to and I hope one day I could present my research as well as you did! Thank you!
Terrific information for RNA-Seq data analysis.
41:41 Anyone know how to obtain the hgnc_symbol? I used cuffdiff which gave me XLOC gene IDs but I can't seem to find a way to effeciciently convert them to common gene names.
Candice, thanks for the video, do you mind sharing the "Presentation.R" script in your video (around 38:35 min)?
Thank you Candice! This has been very helpful. I just about to start an RNAseq experiment and its really great to see the workflow from start to finish.
You are welcome. You can now read the full research article at www.nature.com/articles/s41598-017-16603-y
Thank you so much for sharing your expertise on RNA-seq analysis. Clear and practical explanations. Highly appreciated!!
Thank you for the ellaborate explanation and resources. Most interesting talk I have heard about this topic (RNA-seq)
Thank you for this clearcut guiding in the tremendous world of omics.
Though, the last few minutes of your vid were perhaps the most valuable... Big hug, Candice!
This video is amazing. Thank you so much for sharing it here!
This is a great video I learned a lot! thanks! and I am so sorry for your cat passing away to early. from one cat lover to another, I know the feeling too well, and send you my deepest condolences.
Many thanks Candice Chu for your super clear explanation and your sweet voice :)
Very nice presentation. Thanks for sharing your experience and guidance.
Thanks for the video! It was helpful to me. I also shared it on the r/bioinformatics subreddit as I think others might also benefit from it. The ressources you provide are great, both in quantity and in quality.
Thanks for sharing :)
Hi Candice, firstly, thank you for your video. I'm watching in 2021, but maybe like you I'm stuck in 2016 as my dog and best friend passed away about a month and a half before your cat (1996.01.09-2016.08.14), so I sympathize deeply. Life will never be the same, but I'm trying to throw myself into research to see what I can learn about what it all means...
hi can someone plz explain which file are we using as index file here at 30:03? and what is an index file.
Thank you for your video. This will be useful for starting RNASeq analysis. And congratulations on your paper!
Hi, Candice, thanks a lot for your pretty useful and funny video. If I had a teacher like you, I would conquer RNA-Seq data analysis much earlier.
Thank you for slow and nice presentation
Very useful Candice, thank you for the video and useful resources -definitely helpful - ooo my pug died a while back, I know how you feel...stay blessed!
Thank you for this informative session. It was very helpful for me. I wanted to ask if you have resources available, can I get all.deseq2.R script. I am doing some work with plants around 30 samples.
You are great helpful. It's really interesting that I've already read your post on Biostar 2 weeks before. I thought this guy is really help. Wooh, see you again here in youtube.
Thanks a lot for your detailed explanation. I got the idea how to proceed on this now.
This is a great intro seminar! Thank you, Candice.
This video gave me a thorough introduction to RNA-Seq. Thanks so much Candice!
Thank you very much for all the details. And I like your lecture very much.
Thank you very much for this video. I benefited greatly from this and will definitely try to use the same approach for my project. I'm so sorry you lost your cat; I lost mine 2 weeks ago and I know how it fells
Dear Candice! Thank you so much and may I ask if I can have the complete R script on your vedio. Some of them has been out of the screen.
Awesome work!! Thanks for all the info
Awesome talk for the new player in RNA seq! I am just wondering why RUclips recommends your channel to me later.
Thanks for the upload. Shame about the sound at times. Can you elaborate on why at 20:09 you chose HISAT2 (instead of STAR) for alignment and HTseq (instead of StringTie) for quantifying expression levels and DESeq2 (instead of Ballgown) for differential expression? Thanks!
Hey Tommy, sorry for the late reply. I have been working on finishing my PhD and getting a new job lately. I wasn't very into STAR at the time I was doing the analysis, but now I am aware that more and more people are using STAR for alignment. As for the differential analysis, I briefly mentioned the reason in my paper (see the first comment). Michael Love, the creator of DESeq2, is on Bioconductor ALL THE TIME. He almost immediately answered all my questions. Alternatively, you can use EdgeR, but DESeq2 is more conservative so you get less false postive genes.
Liked your way of disseminating information. Keep it up.
Thank you so much for this talk. It really helped me figure out what tools to explore using for my reserach. And I’m so sorry that your cat passed away.
Hello Chu, may I know if I already have a spreedsheet with FPKM value from excel of my RNA seq data, how shall I generate a DESeqDataSet?
I also have same question...please reply
Im bioinformatic noob i wanna know @30:12. Is where index located? Do i need to create these files before runnign hisat2 right? And right now in manual it is . Is it the same? Thank you in advance
Yes. is the index file. You need to create the index by yourself or download it from HISAT2's website: ccb.jhu.edu/software/hisat2/manual.shtml
Thanks a lot, Candice Chu...Really appreciate it!
Definitely using this my literature review thanks
Great recommendations and resources presented. Thank you.
Hi,Thank you so much Candice! This is a very well structured lecture and I absolutely loved it, I am beginner and I need more help to understand RN sequence analysis.
We need to study a specific cells expression , protein is an end point ..so why the question??
Very good video. Thanks Candice Chu.
Good tutorial for DEG finders. Thanks Candice
Very easy to understand and very helpful! thank you so muchhhh!!
Great presentation for starters. Thanks a lot.
Which file were used for index building using HISAT2-build?
How can we understand that we have less than 12 replicates or not?
Thank you for the wonderful presentation
Hey Candice I’m wondering if your answer to the question about why RNA-seq is used instead of Protein profiling, you mentioned the current technology isn’t sensitive enough to profile all the proteins. But I think RNA- seq has the same problem. Are you able to sequence all the RNA molecules in present in that condition?
Thank you so much for a clear and great presentation
Thanks a lot for this video. Very useful for beginners like me.
Thanks for the video. I need to use a published E. coli RNA seq data to see the particular region of interest. This is to find out the RNA reads in a region of interest. Do you have any video tutorial to do this alignment with the genome and visualize this data?
Great presentation.!!
Hi Candice Thanks for nice tutorial. Is there any tool able to integrate results of proteomics with RNA-Seq?
I am not doing proteomics analysis but you might be able to benefit from this article: www.ncbi.nlm.nih.gov/pmc/articles/PMC3637682/
Thanks for the article. So helpful! Another question; Can a missing biological replicate affect the transcripts abundance and differential expression pattern of genes? How a missing replicate can be dealt during the differential expression analysis?
I am so late here but omg so informative, thank you!
Could you provide the R-code for your analysis? I am quite new to R, but I would love to try and follow.
Good job, thanks for the talk, enjoyed it and got a lot of tips from you!
Thank you, very helpful video!
This was really helpful for me. Thank you.
Great job teaching
Such a great video, i luv this. Thank you Candice
Thank you for this very informative video. It helped me a lot in my project.
This is very nice and very clear, thank you :)
hi, nice video , can you share code by link or mail.
Have you used mixmodel and poisson for DE genes. any video related to that.
Could you please tell me what your controls were in your experimental design?
My controls were age-matched, same-sex, unaffected littermates: www.nature.com/articles/s41598-017-16603-y
Thanks a lot for this nice tutorial. Do you have any suggestions for the fungal RNA Seq analysis or I can still follow the protocol mentioned in the tutorial.
Excellent job, this was very clear!
Good explanation.
Very informative. Kudos!
Thank you so much for your work!
Thank you! Very helpful! Appreciate your work!
Very nice tutorial, thank you so much!
Hi Candice, thanks for upload the video. I have a question, do you know the source where I can upload example of RNA-seq data to practice?
Do you mean download RNA-seq for practice? See this: www.biostars.org/p/111040/
Very interesting lecture:)
Thank you so much, easy to understand with great resources :)
Thank you，very much helpful ！
Hi, Thank you so much for the informative presentation. I have few questions.
Is it possible to calculate t & p values without replicates?
Why some FastQc report gives boxplots without boxes and only lines?
This was really great to help me understand the entire process. I really enjoyed it. Is there a way for me to do this without having access to these packages like hisat2 and HTseq? I don't think I can download them on my computer and even if I did the flies that will be analyzed by this are too big to download. what are my option if I want to do an independent project?
Thanks for the upload, very useful for me.
Thanks, helps a lot!
Thank you so much for this useful video.
Plus sign is a common separator for .fastq reads. :)
Thank you a lot!
It is very useful. Thank you a lot.
This is very useful, thanks!
Thanks, very useful
Hi Candice, this was quite a good intro to the rna seq work flow. Are you giving a talk in Fall 2017 at Tamu ? Thanks again Gig Em
Yes, at TAMU. I did it twice in the same course.
[ RE: read trimming ] Trimming low quality reads isn't as necessary as it once was. Most state-of-the-art aligners (including HISAT2) take quality scores into account and will "soft clip" as needed.
Thanks for your comment!
Awesome, thank you very much
Thank you, your video help me alot