thats the best i ve ever watched on RNAseq. such a quality content...kudos to you..i value the effort you add in this video.cant wait to see your channel grow even bigger..keep it up
@@asifmolbio i wanna learn more about RNAseq and other molecular techniques. how can i join your webinar? if you have some groups where you share about your webinar timing knidly add me
I really appreciate your efforts. Our community needs people like you. It would be more exciting and easy if you cover whole things step by step from start to end.
Best and easy understanding video. I appreciate if you could make a viseo on phylogenetic analysis of miRNA among different living organisms such as plants, algae, fungi, phytoplankton etc
Sir jo mujhe Transcriptome ke sath file milta hai jisme heatmap, kegg and kuch or relationship wale file dete hai oo kya jo hmare samples ke data hote hai ya different.
@@asifmolbio thanks I have made the charts by using this go shiny tool but every enrichment chart is separate how you have combined BP, CC, MF in one figure thats what I want to know.
Hi Dr. Please for my enriched pathways, which one should I choose ( biological pathways, molecular function, or cellular content)? Secondly? How many pathways do you advise me to choose?
@@asifmolbio This video is basically on validation RNAseq with qpcr. I'm not doing qPCR. I'm concerned about how many enriched pathways are advisable to be considered (as in the first 10 or 15 or 20)and which of the gene ontologies (BP,MF,CC) should I consider?
In this video as i have explained it’s depends upon other phenotypic data and literature to choose which genes are responsible for. Similar to this you have to find among the lis which is most suitable for
Sir how can we find protein sequence of one specific protein and then blast in many living organisms like liverworts, algae, fungi, angiosperms and gymnosperms. How we do it?
Very good explanation Dr. Asif. I have a question regarding the word file you have used to explain DEGs. Who will make this word file after getting RNA seq. data from company? student or company?
If we find some novel/candidate genes, how we can find what sort of genes they are or with which genes those novel genes are similar to? And how we can predict their function. Please reply this
Jazakallahu Khairan. was very easy to understand. I have recently conducted RNA seq and have received data from the company but they did not provide such prepared heat maps/ GO/KEGG pathways as you have shown. I would like to know how to assess the raw data into presentable figures. Do you have something to help me with this enormous data set of billions of numerical data?
If you just received the data make sure the company has sent you all the data. In the first instance, usually company sent partial results. Once made sure, please check all the folder there should be all raw data and graphs.
Aoa. I have RNA seq results for resistant and susceptible variety against a pathogen. I have learned alot from this but still i am confused what graphs and pathways should i select for thesis and publication? I have pasted them in new word file infront of each other. but stuck. Can you provide me your email? thanks
Selection of graphs depends on your treatments. I recommend you to watch all videos about interpretation of RNA seq uploaded on my channel. Hopefully, it will be helpful
@@asifmolbio Hello Sir, I have seen your video, and then used ShinyGo, but I did not find any option there to generate a graph with all three component in one graph, they generate separately. I need a graph having all three component (Molecular Biological and Cellular) in one, the same one which you showed in this video. Thanks
thats the best i ve ever watched on RNAseq. such a quality content...kudos to you..i value the effort you add in this video.cant wait to see your channel grow even bigger..keep it up
Happy to read this
@@asifmolbio i wanna learn more about RNAseq and other molecular techniques. how can i join your webinar? if you have some groups where you share about your webinar timing knidly add me
I will add you in scientific writing groups, share your details at
asifalikalas@foxmail.com
Thank you Sir,For sharing the information with us.
The first ever high recommended biology channel in mother language... highly recommend
Thanks
Thank you for explaining in straightforward way. Keep going
Thanks
So clearly explained. I really appreciate Dr. Asif. Pakistan needs such a nice teacher. watching your informative videos from China..
Shazii thanks, glad you like it.
Excellent sir, easy to understand and very logical. Thank you
Thanks Ahmad, glad if its helpful
@@asifmolbio yes, it is...
nicely explained the transcriptomic study, well done, keep up the good work
Glad you like it , keep supporting
Awesome. I really appreciate it
thank you so much for deatiled video, stay blessed
My pleasure
Great work 😍👍👍
Nice work
Highly recommended channel
Thanks
I really appreciate your efforts. Our community needs people like you. It would be more exciting and easy if you cover whole things step by step from start to end.
th-cam.com/video/6sNyNYH_v2U/w-d-xo.html
Here is complete video from start to end
@@asifmolbio Thank you so much.
U r doing wonderful job thanks alot sir love from India
Thanks Gopal, love you back
Best and easy understanding video. I appreciate if you could make a viseo on phylogenetic analysis of miRNA among different living organisms such as plants, algae, fungi, phytoplankton etc
Thanks hopefully i will upload polygenetic series within next two weeks
Hi, do you have an english version of this lecture? Thank you!
Sorry this is the only video on my channel, which is in Urdu. I will upload again with English language version
Thank you
Welcome
May you teach how to use different softwares for RNA seq analysis
nice ❤
Thanks
sir can you please make video of how to find the motifs in rna through which it is bound to a protein in rip seq data using command line
You can search for cis regulatory elements through any database in given gene, then different elements can br search in literature
Hi, do you have the English version of this lecture? I see It's what I need, but I can't understand your language.
oh sorry, thats only video on my channel which is in URDU. How about English subtitles/captions work for you?
Sir jo mujhe Transcriptome ke sath file milta hai jisme heatmap, kegg and kuch or relationship wale file dete hai oo kya jo hmare samples ke data hote hai ya different.
hamry hi samples ka data hota hai yeh
FOR go AND kEGG PATHWAY analysis should we take value based on FC or Padjust?
P adjusted
Hi Sir, How can we make a heat map of selected biological processes or KEGG pathways-related genes?
How to draw heat map for RNA seq data using SR Plot | A free web tool
th-cam.com/video/PxJYcCgDOP8/w-d-xo.html
thank yu, sir,
@@asifmolbio
Nice video how you make this go enrichment charts in a combined way is there any software ?
th-cam.com/video/rOZda0YWZZs/w-d-xo.html
Please check this video, if its helpful
@@asifmolbio thanks I have made the charts by using this go shiny tool but every enrichment chart is separate how you have combined BP, CC, MF in one figure thats what I want to know.
That is done through R program
Hi Dr. Please for my enriched pathways, which one should I choose ( biological pathways, molecular function, or cellular content)? Secondly? How many pathways do you advise me to choose?
You can watch the video below 👇 you will have an idea which to is your final answer
How to select genes for qPCR validation in transcriptome/RNA seq data?
th-cam.com/video/PRhHBcjKAKU/w-d-xo.html
@@asifmolbio This video is basically on validation RNAseq with qpcr. I'm not doing qPCR. I'm concerned about how many enriched pathways are advisable to be considered (as in the first 10 or 15 or 20)and which of the gene ontologies (BP,MF,CC) should I consider?
In this video as i have explained it’s depends upon other phenotypic data and literature to choose which genes are responsible for. Similar to this you have to find among the lis which is most suitable for
HI, can you give us the tutorial of how you performed RNAseq GO analysis using IDEP by GoSeq?
Thank you so much in advance!
Thanks video is already uploaded
iDEP | how to perform RNA seq analysis with no coding
th-cam.com/video/hX6IKZkVyRQ/w-d-xo.html
There is a term cell in cellular component of GO term, what does that define?
Just “cell ?
@@asifmolbio yes...in cellular component category there is a section named cell only
@@mitrabinda1992 its too general category mean anything related to cell you can ignore this terms and focus on others top
Sir mere Transcriptome and metabolics dono ki file aayi analysis karne ke but mujhe samajh nhi aa raha h kaise start kru please help me sir.
A bioinformatics guide to Metabolomic Data analysis interpretation
th-cam.com/video/K2qYuL3l0C4/w-d-xo.html
here is a video of metabolome
if still videos are not helpful, one to one live session can be booked at forms.gle/aEVUtAzrbSHxeN659
If I am comparing between two fruit size then what should be taken as control?
This can be decided by yourself if you any other data to relate
Does the company provide us all DEGs or just RNA sequencing data? If company only provides the data then what software we can use for analysis?
Usually Company provides us with DEGs, even if they did not provide we can filter DEGs with MS excel
❤❤❤
❤️❤️❤️
Sir how can we find protein sequence of one specific protein and then blast in many living organisms like liverworts, algae, fungi, angiosperms and gymnosperms. How we do it?
Open ncbi > go to blastp > paste sequence of your protein and press blast
Very good explanation Dr. Asif. I have a question regarding the word file you have used to explain DEGs. Who will make this word file after getting RNA seq. data from company? student or company?
Company will gave file for all DGEs and students will filter and sort top DGEs by themselves
@@asifmolbio that's great. Thank you brother.
Please do you have the English vision?
Only this viddo is in Urdu rest all are in English
Transcriptomics & Proteomics
th-cam.com/play/PL3fbGvDVm3uspnyI1_RVNtdPDyvInHh1t.html
@@asifmolbio Thanks Dr.
If we find some novel/candidate genes, how we can find what sort of genes they are or with which genes those novel genes are similar to? And how we can predict their function. Please reply this
You can check that gene annotation and look for domains in gene sequence or protein sequence . Moreover gene ontologies can help to predict
Jazakallahu Khairan. was very easy to understand. I have recently conducted RNA seq and have received data from the company but they did not provide such prepared heat maps/ GO/KEGG pathways as you have shown. I would like to know how to assess the raw data into presentable figures. Do you have something to help me with this enormous data set of billions of numerical data?
If you just received the data make sure the company has sent you all the data. In the first instance, usually company sent partial results. Once made sure, please check all the folder there should be all raw data and graphs.
Can you suggest which software/online tools to prepare the KEGG pathway and GO enrichment analysis? Please?
Please see videos about iDEP tool on my channel.
th-cam.com/video/6sNyNYH_v2U/w-d-xo.html
th-cam.com/video/hX6IKZkVyRQ/w-d-xo.html
Aoa. I have RNA seq results for resistant and susceptible variety against a pathogen. I have learned alot from this but still i am confused what graphs and pathways should i select for thesis and publication? I have pasted them in new word file infront of each other. but stuck. Can you provide me your email? thanks
Dear, here is my email asifalikalas@foxmail.com However, i will be replying you on weekends.
Selection of graphs depends on your treatments. I recommend you to watch all videos about interpretation of RNA seq uploaded on my channel. Hopefully, it will be helpful
no english version?
I will upload soon
Hello sir, may you show us how to make gene ontology graph having all three component (Biological, Molecular and Cellular) from sequencing data
th-cam.com/video/rOZda0YWZZs/w-d-xo.html
@@asifmolbio Hello Sir, I have seen your video, and then used ShinyGo, but I did not find any option there to generate a graph with all three component in one graph, they generate separately. I need a graph having all three component (Molecular Biological and Cellular) in one, the same one which you showed in this video.
Thanks
You can download excel list and generate using excel by yourself in combined form.
@@asifmolbio Thanks sir
English version please?
There are individual videos on each of segment please check palylist.
I need ur email id.. i need to ask about processing of array data
asifalikalas@foxmail.com