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- Видео 31
- Просмотров 84 339
BioinfQuests
Индия
Добавлен 25 май 2021
A channel for those who quests for learning Bioinformatics and Biotechnology. I am Priyabrata Panigrahi (PhD), having ~10 years of experience in the field of Bioinformatics. Being passionate about teaching, I thought to use youtube as medium to share knowledge. Please support the channel by subscribing and sharing the content among friends.
You can visit my LinkedIn profile to know more about me.
You can visit my LinkedIn profile to know more about me.
Видео
Learn GREP for Bioinformatics
Просмотров 4511 месяцев назад
In this video, we will be exploring GREP. The data used in this video can be found in drive.google.com/drive/folders/1i-5erARHCaF9kagn7YJw7FBHTO98w3ZD?usp=sharing
SED for Bioinformatics
Просмотров 4611 месяцев назад
In this video we explore SED - The stream editor. The data used in this video can be downloaded here: drive.google.com/file/d/1iLB2X7a06Cspj4QwxBep7gU4CxRZYHsU/view?usp=sharing
AWK for Bioinformatics - Part 2
Просмотров 9411 месяцев назад
This is the part2 of AWK video series. 1st part link: ruclips.net/video/RK4eHs_DyGo/видео.html The file used in this video can be found at drive.google.com/file/d/1QJ9DpXfjuvz_QQBLVt8KwimNkJrUdlEP/view?usp=sharing
AWK for Bioinformatics
Просмотров 28711 месяцев назад
In this video we will explore awk, a widely used programming language in Bioinformatics. The file used in this video can be found at drive.google.com/file/d/1QJ9DpXfjuvz_QQBLVt8KwimNkJrUdlEP/view?usp=sharing
Cell Ranger - Process 10x genomics data (Part2 - Hands-on)
Просмотров 2,9 тыс.Год назад
In this video we will do hands-on of cellranger tool.
Cell Ranger - Process 10x genomics data (Part1)
Просмотров 4,2 тыс.Год назад
In this video we explore cellranger tool which is used to process 10x genomics data. We explore its algorithm, different commands of it. This video is mainly theory. In Part2 we will do hands on.
Challenges in single cell data & how to address them
Просмотров 225Год назад
In this video we will talk about different challenges associated with single cell sequencing data and how to address them.
Single cell technology pipeline - Raw data to Analysis - Overview
Просмотров 641Год назад
In this video we talk in detail how single cell technology works starting from cell capture to sequencing to data processing and analysis. Each of the component plays an import role so it is important to know about them.
Analysis of single cell RNA-seq data - Video series
Просмотров 389Год назад
In this video series, we will explore single cell RNA-seq technology and how to do data analysis in details. This is prepared with an intent for beginners although advanced concepts are also included. Hope this will be useful to you all.
Introduction to single cell sequencing technology
Просмотров 431Год назад
In this video, we will explore difference between bulk and single cell RNAseq sequencing and different applications of the field. 0:00 Introduction 0:24 Bulk vs Single cell 3:41 Application of single cell technology 5:55 Spatial transcriptomics
Violin Plot using ggplot2
Просмотров 9792 года назад
In this video we will explore how to draw violin plot using ggplot2 package. Data used in the video can be downloaded from drive.google.com/file/d/1jcr-yIvUdU6VPswvV9h-x_XLW85q9J8k/view?usp=sharing
Boxplot using ggplot2
Просмотров 1,2 тыс.2 года назад
In this video we will explore how to draw boxplot using ggplot2 package. Data used in the video can be downloaded from drive.google.com/file/d/1jcr-yIvUdU6VPswvV9h-x_XLW85q9J8k/view?usp=sharing
Density plot using ggplot2
Просмотров 2,3 тыс.2 года назад
In this video we will explore - What is density plot, when to use it - How to draw density plot Data used in the video can be downloaded from drive.google.com/file/d/1jcr-yIvUdU6VPswvV9h-x_XLW85q9J8k/view?usp=sharing
Barplot and column plot using R (ggplot)
Просмотров 27 тыс.2 года назад
Barplot and column plot using R (ggplot)
Change Title, Axis labels, legends, Scaling (ggplot2)
Просмотров 9 тыс.2 года назад
Change Title, Axis labels, legends, Scaling (ggplot2)
Facet wrapping of Scatter plot using ggplot
Просмотров 1,5 тыс.2 года назад
Facet wrapping of Scatter plot using ggplot
Add trend lines in scatter plot using ggplot2
Просмотров 6 тыс.2 года назад
Add trend lines in scatter plot using ggplot2
Introduction to Data Visualization using R video series
Просмотров 4102 года назад
Introduction to Data Visualization using R video series
Compare Multiple assemblies using QUAST
Просмотров 2,4 тыс.3 года назад
Compare Multiple assemblies using QUAST
Different Assembly statistics (N50, L50, NG50, LG50, NA50, NGA50 and Misassemblies)
Просмотров 9 тыс.3 года назад
Different Assembly statistics (N50, L50, NG50, LG50, NA50, NGA50 and Misassemblies)
Canu: Long Read Genome Assembly Tool
Просмотров 2,7 тыс.3 года назад
Canu: Long Read Genome Assembly Tool
WTDBG2: Long Read Genome Assembly Tool
Просмотров 5823 года назад
WTDBG2: Long Read Genome Assembly Tool
Miniasm: Long Read Genome Assembly Tool
Просмотров 5663 года назад
Miniasm: Long Read Genome Assembly Tool
Flye: Long Read Genome Assembly Tool
Просмотров 2 тыс.3 года назад
Flye: Long Read Genome Assembly Tool
Shasta: Long Read Genome Assembly Tool
Просмотров 6733 года назад
Shasta: Long Read Genome Assembly Tool
Long Read Genome Assembly Video Series
Просмотров 7313 года назад
Long Read Genome Assembly Video Series
youre goated
Great video
Good job, looking forward for more R contents.
Thank you sir. Very nicely done ! More lectures sir !
I feel like this is an excellent video but I can barely hear you man
Mean and median here is different here. But both are different parameters (one is gene and other is reads) and cannot be compared.
Hi. Thanks for the feedback. Do you mean the 2 qc parameter? Total umi and total genes in the violin plot? Yes they can't be compared directly via violin plot since y axis is different for both. The correlation plot is helpful to see how much correlation you see. Usually correlation is high. I hope I understood your point of view.
Thank you!!!
I want to do this on my own data beause we have our own sequencing machice and we do the sequencing inhouse so is it possible to genrate a counts data using cellranger
Yes cell ranger pipeline starts from fastq to count. U can refer the 2nd part of this video to know more.
@@bioinfquestsI am reaching out to inquire about Cell Ranger and its compatibility with our in-house sequencing setup. We currently have our own sequencer and would like to explore the possibility of using Cell Ranger to generate counts from our own BCL data. As I have limited hands-on exposure in library preparation, I wanted to understand if any modifications or changes are required in the library preparation process to use Cell Ranger effectively. Could you please provide some insights into how Cell Ranger works and whether it can be seamlessly integrated with our existing library preparation workflow?
Excellent tutorial. I appreciate you showing how samples are set up on the chip.
Glad it was helpful!
Thank you sir. Very well explained.
It's super useful! I was looking for some information like this since I'm more a computing side but is doing collaboration with people using 10X, which I have not much knowledge about. Thank you so much for your work!
It was soo soo soo easy with your explanation literally i am a new student and i didn't even listen about cell ranger but you made it extremely easy and honestly i will follow and watch your tutorials.
Thanks for encouraging feedback. Appreciate if you shout out about my channel in your network. This will boost my channel. I will soon be posting some videos on seurat.
ERROR: Permission denied: couldn't open MRO file sir I am getting this error, what to do ?
What is the citation/paper at 1:37. Excellent diagram!
If I am not wrong it's www.nature.com/articles/s41596-018-0073-y Is this video useful? Any positive or negative feedback would be valuable.
@@bioinfquests Yes, this video is very useful! I keep coming back to it. :D THANK YOU!!
Thank you. i am going to be learning this analysis, i am a beginner and please do not leave providing us with these lovely tutorials
Thanks for your encouraging feedback. Please share about my channel in your network. This will boost my channel. Yes I will soon be posting some videos on seurat.
Hi, do I need linux to run this program or can I run it on macOS?
Most of these tools can be installed on macos also. So u can run on macos.
Kal mere presentation hai .pagal hogya tha me . thank you so much ❤️❤️ for this video
Dear Sir, Thank you for such a nice explanation
Can you please make a vidoe tutorial on k mergenie
Thank you for this video. I wonder how we can evaluate the best one?
Thank you for the video, although the concept of NA50 is not clear, and you didn't mention how to calculate it. Another thing is that you didn't mention how to evaluate correctness!! The video is quite naive and with very basic information, but thank you anyway.
This very helpful thank you
That was absolutely helpful 👌
what are the units of N50 guys ?
bp basepairs
how to italisize part of axis labels only?
I was waiting for the main title, I want to change the position, font type, and font size how will I go about it
For text size, u can use element_text function and set size parameter. for font type, use family parameter.
It is so rare for me to get a video definition this concise and easy to understand. Thank you so much.
For context I’m a computer scientist who is doing research into computation biology. I have almost no biology background so videos like this make my life so much easier when reading papers
Sir.. Your bioinformatics video on genome assemblies is very helpfull and informative. I have little query that how to create FastqToFasta itself. When I run FastqToFasta its showing commond not found. What does it mean? And give the link to download the fastq file.
Thanks. Fastq file link is provided in the description. The fastqtofasta is provided by shasta. it will be there in the shasta installation directory. you need to use full path to the script or copy the script in the data folder and run from there
Thanks sir for the reply and valuable suggestions. I will try.
Sir..can you provide any classes or traning on the hands on linux bioinformatics? Pls provide your contact No.
Thank you so much for making these videos. Compared to other videos on youtube, your videos are very easy to understand as you go through the description without making it too complicated. I really appreciate your efforts to help learners like us. Can you please also make videos on how to perform different statistical tests using R studio? Thanks again!
Very useful. Thanks a lot!
I’m wondering what values were being used for the y axis in the stacked bar plots when the y axis wasn’t specified.
Its the count of each category which is specified on x axis. it will be automatically counted. When we specify x with a column, R will xount frequency of each category and consider that as y. Hope it answers.
Thank you for this, amazing explanation.
What will be the code if we want to do the same with excel data
Better to save the data of excel in tab separate value or comma separated csv file and use same read.table or read.csv method to load the data in df and plot. Although there are package like gdata or xlxs are there which can be used to read excel data.
Nicely explained
Useful for economics as well. Thank you
Very helpfull video!. I have a question, why do not you use a reference genome to assembly?
See there are 2 possibilities 1. You have reference genome already known e.g. human. 2. You do not have reference genome e.g. a new species is identified and you plan to sequence them. In former case you can use already known genome reference information to guide the assembly process. In second case, you are newly doing assembly to generate reference genome. In first case at least you can compare the assembly with reference to infer how close your sample is with the reference one while in second case you have to trust or validate the assembly based on assembly statistics or some other literature evidence or prior experimental evidence.
The most useful video I have seen on this topic. No jokes.
Very nice video my friend. You are the Lionel Messi of R coding.
@BioQuests :-) Thanks for knowledgeable videos... It's make my lots of basic fundamental things very clear and crystal. Just request you to have some videos on data labels in charts as some of data needs to represent with numbers.
Yes am planning to add few videos. Thanks for the suggestions.
Get this man more subscribers
Thanks you a lot please can you do same exemples using temperatures data
Thank u for this I have this bar plot that makes frequency of categories Given the database is 250k, i have very long frequncy labels that when plotting get mixed with other frequencies. How to change them? Say divid frequencies by 1000
How many categories u are getting. If i understood correctly u r saying that you have so many categories, each bar overlap with nearby bar? Can you elaborate more since its not clear. If you are saying that y axis value is high, you can represent frequency as percentage as well.
@@bioinfquests i have about 6 categories, when i do bar plot, the results are the count of each category. the length of the database is 250,000 rows. when I do count for these categories the frequency i.e. number get mixed up
Sorry not able to understand what number gets mixed up means..since there are 6 categories and total 250k values, u will get 6 frequency values which will add to total 250k. So it should plot fine, x being the category and y being the value.
@@bioinfquests hi thank you for this. I have about 6 categories i.e. bars and the dataset is very long 250,000 records. so when I have some of them use numbers in the 100,000 the get mixed up. wonder if i make adjustments to make numbers display well without getting inter linked. I actually thought of making the division in the dataset now by 1000 for example
@@ahmed007Jaber you can display the frequency as percentage as well so that y axis will be in the scale of 0-100.
Thanks man, I´m from Colombia and this video help me so much! :3
Thank you. Please share among your network and social media to reach out to wider audience. Appreciate it. Thanks again.
Thank you for all the videos. Its quite helpful.
Thank you Mustafa. Pls share among your network to reach out to wider audience. Thank you. Appreciate it.
Excellent!
Thanks Shaminur. Please share in your network to reach out to wider audience. Thank you. Appreciate it.
good video. thanks.
Thanks Saygin. Request you to support channel by subscribing and getting notification for upcoming videos.
Thanks for this informative walkthrough.👍🏾
Thank you Soji. Appreciate if you can support the channel by subscribing if not done. Will be posting many interesting topics in future.
Thanks again, could you please explain about valcano plot and it’s graphs?
Thanks for the suggestion. Will keep this in mind and create a session on this.
thank you so much!
indian makes everything easier thanks
Thanks Arsham. Please subscribe to channel. Am planning to post other sessions in coming weeks. Subscribe to get notifications.