What is Strandedness in RNA-Seq data? | RNA-Seq Stranded Library Construction Methods

Рет қаралды 5,647

Күн бұрын

In this video I talk about what is strandedness in RNA-Seq data, what additional information do stranded data provide us. In addition, I compare stranded and unstranded RNA-Seq library preparation methods, discuss the terminologies associated with them. Lastly, I also talk about various ways one can determine strandedness in RNA-Seq data.
I hope you find this video helpful! Leave your thoughts in the comment section below!
Parameters for strandedness in various RNA-Seq tools:
rnabio.org/module-09-appendix...
Chapters:
0:00 Intro
1:03 Why do we need strand-specific information from RNA-Seq reads?
4:45 A typical RNA-Seq experiment workflow
5:30 Strandedness in transcription
6:39 Library Preparations methods - unstranded and stranded protocols explained
10:08 How are reads stored in a .fastq files for each method?
11:05 Terminologies
11:59 Ways to determine strandedness from RNA-Seq data
You can show your support and encouragement by buying me a coffee:
www.buymeacoffee.com/bioinfor...
To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: khushbu_p@hotmail.com
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Пікірлер: 23

@tolga1292 Жыл бұрын

Wonderful! Could you talk about STAR in your next video?

@tolga1292 Жыл бұрын

In addition with Post-alignment-QC would be wonderful :)

@AndazeBayan1 Жыл бұрын

Just like your name, your work's khusbu is reaching to those who need it the most ❤ Keep doing this great work.

@hridayhomechowdhury2142 Жыл бұрын

Thank you very much, I learned a lot from your tutorials.

@user-zg2uf2od7n Жыл бұрын

Thanks a million, Khushbu! Kindly keep creating these videos and go ahead for the IGV video please!

@ThaoNguyen-sv2rg 10 ай бұрын

Great video Khushbu ! 6:14 Based on your explanation, for mRNA1, the antisense should be 3'5' and sense should be 5'3'. Do I misunderstand or is it the slide misrepresentation ? Thank you

@gadhakleons 6 ай бұрын

I had the same question.. Were you able to clear that?

@sjwu571 29 күн бұрын

Hi loved your videos. Just want to point out, at 6:28, I think your labeling for Gene 1 is wrong. Please double check I'm not crazy. Thanks!

@tushardhyani3931 Жыл бұрын

Thank you ma'am !!

@reinhardgrausenburger4095 11 ай бұрын

Great Video! It would be great if you could also show us how to check strandness in IGV. Thanks a lot!

@divyaagrawal6740 Жыл бұрын

Thank you for the video Khushbu :)

@apostolosevgeniospavlos320 Жыл бұрын

Perfect presentation for someone who want to understand the differences between stranded and unstranded protocols. I have one question, how it is possible to understand the strandedness from GeneCounts option coming from STAR. In case of unstranded data it is clear that you ll choose the first column, but in case of stranded data how can you determine which column you choose between 2nd and 3rd?

@hinasultana2066 2 ай бұрын

Very nice presentation. I have a question. In stranded RNASeq, after the second strand cDNA is synthesized with dUTP, it is degraded. I am confused as to how the second strand information is generated later on , when that strand was degraded?

@perthteluguchronicles Жыл бұрын

Thank you very much, I learned a lot from your tutorials. Can you make a tutorial on aberrant splicing events using FRAZER please

@aayushividhoy5943 Жыл бұрын

Hi your videos are soo good am currently preparing for a job in bioinformatics...if possible can you please guide us like what kind if questions will be asked and how we should prepare for an interview