Thank you sir. Very nicely done ! More lectures sir !
@5602KK10 ай бұрын
I feel like this is an excellent video but I can barely hear you man
@aram845810 ай бұрын
Mean and median here is different here. But both are different parameters (one is gene and other is reads) and cannot be compared.
@bioinfquests10 ай бұрын
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.
@TWA35610 ай бұрын
Thank you!!!
@AnkitYadav-v2v8z10 ай бұрын
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
@bioinfquests10 ай бұрын
Yes cell ranger pipeline starts from fastq to count. U can refer the 2nd part of this video to know more.
@AnkitYadav-v2v8z10 ай бұрын
@@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?
@King_of_carrot_flowers11 ай бұрын
Excellent tutorial. I appreciate you showing how samples are set up on the chip.
@bioinfquests10 ай бұрын
Glad it was helpful!
@orbitaaltube11 ай бұрын
Thank you sir. Very well explained.
@thuongpham8912 Жыл бұрын
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!
@maidach6964 Жыл бұрын
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.
@bioinfquests Жыл бұрын
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.
@sanjaisrao484 Жыл бұрын
ERROR: Permission denied: couldn't open MRO file sir I am getting this error, what to do ?
@2007dolphinlover Жыл бұрын
What is the citation/paper at 1:37. Excellent diagram!
@bioinfquests Жыл бұрын
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.
@2007dolphinlover Жыл бұрын
@@bioinfquests Yes, this video is very useful! I keep coming back to it. :D THANK YOU!!
@hossainadamzad5907 Жыл бұрын
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
@bioinfquests Жыл бұрын
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.
@maxchung5015 Жыл бұрын
Hi, do I need linux to run this program or can I run it on macOS?
@bioinfquests Жыл бұрын
Most of these tools can be installed on macos also. So u can run on macos.
@brahmaganeswar6264 Жыл бұрын
Kal mere presentation hai .pagal hogya tha me . thank you so much ❤️❤️ for this video
@muhammadakmal1414 Жыл бұрын
Dear Sir, Thank you for such a nice explanation
@sawiq802 Жыл бұрын
Can you please make a vidoe tutorial on k mergenie
@muhammadakmal1414 Жыл бұрын
Thank you for this video. I wonder how we can evaluate the best one?
@QAKS1264 Жыл бұрын
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.
@benaawf9227 Жыл бұрын
This very helpful thank you
@lody33100 Жыл бұрын
That was absolutely helpful 👌
@victorrorisang479 Жыл бұрын
what are the units of N50 guys ?
@МарияФролова-т7я Жыл бұрын
bp basepairs
@bimalkumarchhetri40122 жыл бұрын
how to italisize part of axis labels only?
@brightamenu16172 жыл бұрын
I was waiting for the main title, I want to change the position, font type, and font size how will I go about it
@bioinfquests2 жыл бұрын
For text size, u can use element_text function and set size parameter. for font type, use family parameter.
@jimmyjam23732 жыл бұрын
It is so rare for me to get a video definition this concise and easy to understand. Thank you so much.
@jimmyjam23732 жыл бұрын
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
@rakeshkumargupta8012 жыл бұрын
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.
@priyabrata85782 жыл бұрын
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
@rakeshkumargupta8012 жыл бұрын
Thanks sir for the reply and valuable suggestions. I will try.
@rakeshkumargupta8012 жыл бұрын
Sir..can you provide any classes or traning on the hands on linux bioinformatics? Pls provide your contact No.
@msrahman2 жыл бұрын
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!
@AmrateMoustafa2 жыл бұрын
Very useful. Thanks a lot!
@sc00badive2 жыл бұрын
I’m wondering what values were being used for the y axis in the stacked bar plots when the y axis wasn’t specified.
@bioinfquests2 жыл бұрын
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.
@alfredoderodt65192 жыл бұрын
Thank you for this, amazing explanation.
@Acoustics1952 жыл бұрын
What will be the code if we want to do the same with excel data
@bioinfquests2 жыл бұрын
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.
@drvijaykamal2 жыл бұрын
Nicely explained
@adamw20302 жыл бұрын
Useful for economics as well. Thank you
@marimbadearcomasaya32192 жыл бұрын
Very helpfull video!. I have a question, why do not you use a reference genome to assembly?
@bioinfquests2 жыл бұрын
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.
@ifeanyiattamah81212 жыл бұрын
The most useful video I have seen on this topic. No jokes.
@joro24172 жыл бұрын
Very nice video my friend. You are the Lionel Messi of R coding.
@chandrasingh58562 жыл бұрын
@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.
@bioinfquests2 жыл бұрын
Yes am planning to add few videos. Thanks for the suggestions.
@emmanuellebeling85512 жыл бұрын
Get this man more subscribers
@Hamza_Muhamadson2 жыл бұрын
Thanks you a lot please can you do same exemples using temperatures data
@ahmed007Jaber2 жыл бұрын
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
@bioinfquests2 жыл бұрын
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.
@ahmed007Jaber2 жыл бұрын
@@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
@bioinfquests2 жыл бұрын
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.
@ahmed007Jaber2 жыл бұрын
@@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
@bioinfquests2 жыл бұрын
@@ahmed007Jaber you can display the frequency as percentage as well so that y axis will be in the scale of 0-100.
@nicolastovar81212 жыл бұрын
Thanks man, I´m from Colombia and this video help me so much! :3
@bioinfquests2 жыл бұрын
Thank you. Please share among your network and social media to reach out to wider audience. Appreciate it. Thanks again.
@jakkaas12 жыл бұрын
Thank you for all the videos. Its quite helpful.
@bioinfquests2 жыл бұрын
Thank you Mustafa. Pls share among your network to reach out to wider audience. Thank you. Appreciate it.
@md.shaminurrahman87582 жыл бұрын
Excellent!
@bioinfquests2 жыл бұрын
Thanks Shaminur. Please share in your network to reach out to wider audience. Thank you. Appreciate it.
@saygndiler57342 жыл бұрын
good video. thanks.
@bioinfquests2 жыл бұрын
Thanks Saygin. Request you to support channel by subscribing and getting notification for upcoming videos.
@sojiademiluyi43062 жыл бұрын
Thanks for this informative walkthrough.👍🏾
@bioinfquests2 жыл бұрын
Thank you Soji. Appreciate if you can support the channel by subscribing if not done. Will be posting many interesting topics in future.
@arshammikaeili74082 жыл бұрын
Thanks again, could you please explain about valcano plot and it’s graphs?
@bioinfquests2 жыл бұрын
Thanks for the suggestion. Will keep this in mind and create a session on this.