Jazakillahi khayran again! Such a blessing and barakah to come across your video Alhamdulillah. 2 questions: 1. I see you have used rice data. Since I am working with pearl millet and there are no annotations for pearl millet as yet, would it be possible to use iDEP for analysis? 2. I have data that has mapped the pearl millet genes to rice and Arabidopsis. should I use this instead? As salaam wa alikum.
Wslam 1. Yes hopefully it would be possible 2. No need to select any specie. Let the system automatically detect best matching specie according to gene IDs.
I am a Bioinformatics degree student 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 so much Sir. I was so depressed and worried about the data analysis because I had no idea about it but after watching your amazing videos. I feel like I can do the analysis. Thank you so much. May you get more success. ameen
Dear Dr Asif. Thank you for providing such an insightful tutorial on web-based RNA-seq data processing. I would like to inquire about how to convert the list of those query IDs into the corresponding gene symbols according to the human reference genome?, opening a new targeted direction for further exploratory experimental studies.
Hi @ Dr. Asif's Mol. Biology, thanks a lot for such an interactive tutorial. I have emailed you my queries about RNA seq analysis. Your time and response would be highly appreciated. Many thanks
Very helpful video for someone who has the raw read counts in hand. Could you please show us how to do pathway enrichment analysis using list of upregulated and downregulated genes with logFC and P value on excel
JAZAK ALLAH U KHAIR asif bhai you are doing a great work. ALLAH RABULL bless you in this world and hereafter. Please i have a question that at 3:00 minutes you select oryzae sativa. My specie is locust but i cannot find in the best match option. Please can you help me regarding this matter. I shall be very thankful to you.
Wonderful job Dr Asif, Juts wonder could you help me in solving my query? can you plz guide how can one access authentic RNA sequence? like I want to analyse few genes.
if you need to upload FC value, you can use mean and mean expressions. You can calculate the mean in Excel. Otherwise, you can directly choose expression values and gene IDs it will automatically calculate the mean
@@asifmolbio Generally replication, transcription and translation occurs in our and plant cells 24/7 and when we extract mRNA obviously some of the mRNA are in the translation stages at the same time when we extracted mRNA from our cell and during translation, ribosome machinery is attached to the mRNA?
Yes normally transcriptome refers to multiple forms of RNAs including ribosomal. But wo do poly A tail enrichment to identify mRNAs as rRNA removal enables higher sequencing depth of mRNA, leading to better detection of transcripts. This is critical for analyzing differential expression, particularly when detecting non-coding or lowly expressed RNAs.
It's not accepting file second time, first time it showed results like you but second time not uploading or reading data file. What is the reason? How can we do it same?
Hello. I am a Ph.D. student. Have you made any tutorial video for GO annotation analysis and KEGG enrichment analysis? If yes, can you please send me the link.
Dear Dr. Asif Ali, I hope my message will find you in good health. I have an issue while using iDEP, when I click on pathway it shows "no significant pathway found" and when I move to "Genome" option it shows "Error: An error has occurred. Check your logs or contact the app author for clarification". Please guide
Thank you of your Video. I have one question I need to prepare interactome of the protein base of the RNA seq, but I don't know by IDEP tool, can I prepare or not?
Hi thanks for such an informative and educational video. Can I generate the diagrams shown in the video using the 16S rRNA sequence data? If so, how do I then prepare my CSV file? What columns must I put on the excel sheet in such that I will be able to submit it on this platform and generate similar figures in this video?
@@asifmolbio Thank you for your prompt response. I am working with bacterial species and I don't see any option available for bacteria. May I kindly get your email address so I can send you my query please?
@@asifmolbioyes I do have the read count and I did the gene expression analysis using idea. However, I can’t do the GO, KEGG and other analyses as idep do not recognise the gene id.
How can we retrieve rna sequence ? You said company ! Which company ..can we get the sequence online From any tool by putting the dna sequence or other ???
You can retrieve the raw sequence of RNA. Please be informed that there are many companies (TShengke, BioRAD and many more) which perform RNA seq analysis of your samples.
Hello dear, How can one download publicly available datasets, and use that here? Because they contain many files or data, so what are useful and how to select or choose one from there. Can you elaborate? Thanks
1.RNA-seq raw datasets can be downloaded from NCBI SRA toolkit. 2. If we use our windows system then we will have many options to download and will cause trouble. 3. With the use of Ubuntu (virtual machine system) we can easily download our required data by just putting NCBI accession number.
@@asifmolbio The way you deliver these lectures are very informative and helpful, a video should be made on how to access geo datasets... You should share such informative tutorials, your way of doing things are amazing 👏... Thanks
Hi one quick question! I uploaded the CSV file with read counts and gene IDs. It shows a warning for sequence depth bias and states that the total read counts are significantly different between sample groups. What does it mean? How to take this in account when analyzing data? I do have 4 groups and total 23 samples! Thanks
Sir.. Currently i completed transcriptome analysis and results were obtained. I want to mine my gene of interesr from the entire transcripts.. One of the annotated contigs include the gene of ineterst. But some of the terminal sequences were missing. So how can i completely get that sequence
Because the terminal sequences combined with adapters are trimmed knowingly, RNA transcripts will give you only expressing data why you want to use this for sequence retrieval
Hello Sir I have fold change data , without corrected P values , when I use this option on iDEP for network construction no figure is produced. I have 100 genes and two samples. Kindly help
is there any software for Proteomics data analysis like this, then please make a tutorial for proteomics data. if not then please mention the name of the software. Jazak Allah
@@asifmolbio thank you for answering. BTW I have seen all of your videos and I check your channel time to time, but I couldn’t find any platform where we can run our proteomics cvs file like this video and get the desired plot. If possible then please guide me. JazakAllah
Hello Dr. Asif, thanks for the informative video, I am trying to analyze a ".txt file" I downloaded from GEO database " GSE49110". I am unable to understand how to arrange the data columns in an excel file. I am getting errors during the DEG1 analysis.
@@asifmolbio Thank you so much. It really helped. Maybe you can make a video using cancer gene expression data. I am sure It would be of interest to many of us.
Jazakillahi khayran again! Such a blessing and barakah to come across your video Alhamdulillah.
2 questions:
1. I see you have used rice data. Since I am working with pearl millet and there are no annotations for pearl millet as yet, would it be possible to use iDEP for analysis?
2. I have data that has mapped the pearl millet genes to rice and Arabidopsis. should I use this instead?
As salaam wa alikum.
Wslam
1. Yes hopefully it would be possible
2. No need to select any specie. Let the system automatically detect best matching specie according to gene IDs.
@@asifmolbio Sir, would you make a video on how to conduct weighted gene co-expression network analysis (WGCNA)?
This is very imp
I am a Bioinformatics degree student 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 :)
Sir while uploafing the csv file it always showing disconnected from the server
Thank you so much Sir. I was so depressed and worried about the data analysis because I had no idea about it but after watching your amazing videos. I feel like I can do the analysis. Thank you so much. May you get more success. ameen
Thanks Bira, glad if it’s helping
Really impressive informative and expresses your vast knowledge about your field
zabardast yar I will watch this full video tonight
glad if its helpful
looking informative for my upcoming samples from china
Dear Dr Asif. Thank you for providing such an insightful tutorial on web-based RNA-seq data processing. I would like to inquire about how to convert the list of those query IDs into the corresponding gene symbols according to the human reference genome?, opening a new targeted direction for further exploratory experimental studies.
ruclips.net/video/b_042ZbXTwU/видео.html
God bless you,you lecture is 100%,
Thanks stay connected
@@asifmolbio i have some question,if possible plz share your wechat or whatsapp,i appricated your hard work
Hi @ Dr. Asif's Mol. Biology, thanks a lot for such an interactive tutorial.
I have emailed you my queries about RNA seq analysis. Your time and response would be highly appreciated. Many thanks
ok let me check and respond to email
Thank you, Dr. Asif Bhai, It's really helpful for my work.
I am glad if it's helpful.
thanks for a nice lecture
Glad you like it
Very helpful video for someone who has the raw read counts in hand. Could you please show us how to do pathway enrichment analysis using list of upregulated and downregulated genes with logFC and P value on excel
Glad you like it.
ruclips.net/video/rOZda0YWZZs/видео.html
very very helpful.
Glad you like it
JAZAK ALLAH U KHAIR asif bhai you are doing a great work. ALLAH RABULL bless you in this world and hereafter.
Please i have a question that at 3:00 minutes you select oryzae sativa. My specie is locust but i cannot find in the best match option. Please can you help me regarding this matter. I shall be very thankful to you.
Wslam thanks waqas, i think your specie is not listed your specie genome is sequenced?
Very informative video.. Thanks Dr Asif. I have one question..How can we convert gene id into gene name?
which specie or organism you need to change?
thank you very much. super helpful tool!
Glad you like it
We’ll explained
Hello, very useful tutorial. May I know whether I can use it for the analysis of mi-RNA nanostring data?
Yes can be used
sir i find your video very interesting and clear explanation. could you make a video on MA plot.
Sure Dipen, will make soon
Wonderful job Dr Asif, Juts wonder could you help me in solving my query? can you plz guide how can one access authentic RNA sequence? like I want to analyse few genes.
Thanks you like it, what you mean by authentic sequence?
while uploading the values, there are 3 replicate values for WT and MT. How can we take mean of three samples to proceed. I didnt get it.
if you need to upload FC value, you can use mean and mean expressions. You can calculate the mean in Excel.
Otherwise, you can directly choose expression values and gene IDs it will automatically calculate the mean
Nice and informative videos 👍
Please make a video for tcgadata differential gene expression analysis with r
Thanks parkash,glad you like it. I have noted down your video topic stay connected
Hi, Thanks for very good video.
Can you please tell me if our RNA-seq sequences contain only mRNA or pre-mRNA or mRNA with the ribosomes?
Only mRNAs
@@asifmolbio
Generally replication, transcription and translation occurs in our and plant cells 24/7 and when we extract mRNA obviously some of the mRNA are in the translation stages at the same time when we extracted mRNA from our cell and during translation, ribosome machinery is attached to the mRNA?
Yes normally transcriptome refers to multiple forms of RNAs including ribosomal. But wo do poly A tail enrichment to identify mRNAs as rRNA removal enables higher sequencing depth of mRNA, leading to better detection of transcripts. This is critical for analyzing differential expression, particularly when detecting non-coding or lowly expressed RNAs.
It's not accepting file second time, first time it showed results like you but second time not uploading or reading data file. What is the reason? How can we do it same?
Must be some errors in formatting, watch video about how to design file for iDEP
Thank you sir
You are welcome
It's a good video, please can I upload DEG list? if yes kindly explain to me how to do it and compare multiple data and not just a pair
What you mean multiple data ?
Hello. I am a Ph.D. student. Have you made any tutorial video for GO annotation analysis and KEGG enrichment analysis? If yes, can you please send me the link.
ruclips.net/video/rOZda0YWZZs/видео.html
Dear Dr. Asif Ali,
I hope my message will find you in good health. I have an issue while using iDEP, when I click on pathway it shows "no significant pathway found" and when I move to "Genome" option it shows "Error: An error has occurred. Check your logs or contact the app author for clarification". Please guide
Please send your excel DEGs file to me in email
Thank you of your Video. I have one question I need to prepare interactome of the protein base of the RNA seq, but I don't know by IDEP tool, can I prepare or not?
Interactome cannot be prepared using iDEP
❤❤❤❤❤❤❤❤❤
❤️
Hi sir,can we write a research paper using data from NCBI by incorporating this tool
Off course but clearly mention the source of data in materials and methods section
@@asifmolbio thanks sir
Hi thanks for such an informative and educational video.
Can I generate the diagrams shown in the video using the 16S rRNA sequence data?
If so, how do I then prepare my CSV file? What columns must I put on the excel sheet in such that I will be able to submit it on this platform and generate similar figures in this video?
if you have data of 16S rRNA sequence ID (similar to NCBI ) and reads counts data or fpkm valuse you can use iDEP for analysis.
@@asifmolbio Thank you for your prompt response. I am working with bacterial species and I don't see any option available for bacteria. May I kindly get your email address so I can send you my query please?
asifalikalas@foxmail.com
@@asifmolbioyes I do have the read count and I did the gene expression analysis using idea. However, I can’t do the GO, KEGG and other analyses as idep do not recognise the gene id.
How can we retrieve rna sequence ? You said company ! Which company ..can we get the sequence online From any tool by putting the dna sequence or other ???
You can retrieve the raw sequence of RNA. Please be informed that there are many companies (TShengke, BioRAD and many more) which perform RNA seq analysis of your samples.
We have to mention this website i our manuscript writing?
doi.org/10.3390/ijms23147887
I have used this website and published an article
You can read
Wow 👍👍👍👍🥰🥰🥰🥰🥰
Glad you like it
Hello dear,
How can one download publicly available datasets, and use that here? Because they contain many files or data, so what are useful and how to select or choose one from there.
Can you elaborate?
Thanks
1.RNA-seq raw datasets can be downloaded from NCBI SRA toolkit.
2. If we use our windows system then we will have many options to download and will cause trouble.
3. With the use of Ubuntu (virtual machine system) we can easily download our required data by just putting NCBI accession number.
@@asifmolbio The way you deliver these lectures are very informative and helpful, a video should be made on how to access geo datasets...
You should share such informative tutorials, your way of doing things are amazing 👏...
Thanks
Thanks, stay in touch i will make on this topic too very soon InshaAllah
👍
Hi one quick question! I uploaded the CSV file with read counts and gene IDs. It shows a warning for sequence depth bias and states that the total read counts are significantly different between sample groups. What does it mean? How to take this in account when analyzing data? I do have 4 groups and total 23 samples! Thanks
It shows your technical replicates have significant reads counts, no problem, you can move ahead to follow up analysis and see how PCA works
Sir plz make a vedio for creation of cvc file formating
ruclips.net/video/hX6IKZkVyRQ/видео.html
Sir.. Currently i completed transcriptome analysis and results were obtained. I want to mine my gene of interesr from the entire transcripts.. One of the annotated contigs include the gene of ineterst. But some of the terminal sequences were missing. So how can i completely get that sequence
Because the terminal sequences combined with adapters are trimmed knowingly, RNA transcripts will give you only expressing data why you want to use this for sequence retrieval
@@asifmolbio Thank you sir.. But the sequence which trimmed include a portion of my gene of interest.. So what can i do
@@asifmolbio if possible pls give ur persinal email id sir
asifalikalas@foxmail.com
@@asifmolbio thanku sir
Taz Uddin
Hello Sir
I have fold change data , without corrected P values , when I use this option on iDEP for network construction no figure is produced. I have 100 genes and two samples. Kindly help
iDEP | how to prepare design file | problems
ruclips.net/video/hX6IKZkVyRQ/видео.html
Please check this video if its helpful for you
it is very informative but Dr. sb it is not best for bigdata analysis...
Its ever updating, but still very handy to use
@@asifmolbio no doubt it’s very easy to use but at then end of uploading data server error
Try to perform on only DEGs list
How can I do idep for wheat data?
ruclips.net/video/hX6IKZkVyRQ/видео.html
Please watch this video
👏🏼
Thanks
Could you please share a video about evaluating RNA data and associating it with the disease?
How to analyze public RNA-seq datasets using iDEP tool
ruclips.net/video/BI56K3gYdds/видео.html
is there any software for Proteomics data analysis like this, then please make a tutorial for proteomics data. if not then please mention the name of the software. Jazak Allah
How to interpret the results of proteomics data analysis? Proteomics Data interpretation
ruclips.net/video/e8VOm8YFhkA/видео.html
Check out the above video JezakAllah
@@asifmolbio thank you for answering. BTW I have seen all of your videos and I check your channel time to time, but I couldn’t find any platform where we can run our proteomics cvs file like this video and get the desired plot. If possible then please guide me. JazakAllah
Hello Dr. Asif, thanks for the informative video, I am trying to analyze a ".txt file" I downloaded from GEO database " GSE49110". I am unable to understand how to arrange the data columns in an excel file. I am getting errors during the DEG1 analysis.
How to analyze public RNA-seq datasets using iDEP tool
ruclips.net/video/BI56K3gYdds/видео.html
@@asifmolbio Thank you so much. It really helped.
Maybe you can make a video using cancer gene expression data. I am sure It would be of interest to many of us.
How I recieve data ?? From where??
ruclips.net/video/BI56K3gYdds/видео.html
Watch this
Thank uu sir
I want the data of Takifugu rubripes. How can I get that ??? Sir plzz tell me
Please watch the video, follow the method if your specie is available
brother where are you doing job, how I contact you
I am working as Postdoc in China
ISRARUL HAQUE
send me your email please
Name:Emmanuel kalumbu
send me your email please
Please reply sir please
I have sent you a video link it will help you to analyze your specie
Thanks sir