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RNA Seq / Transcriptome data analysis with a webtool | iDEP tool 

Dr. Asif's Mol. Biology
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#RNA #rnaseq #analysis #transcriptomedata #IDEP
In this video, I have given a demo of webtool tool (IDEP) that can be used for complete RNA seq data analysis. This web tool does not require any software or any R language Package.
This too can be accessed at this website
bioinformatics....
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5 окт 2024

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Комментарии : 131   
@4Getf00l
@4Getf00l Год назад
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.
@asifmolbio
@asifmolbio Год назад
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.
@4Getf00l
@4Getf00l Год назад
@@asifmolbio Sir, would you make a video on how to conduct weighted gene co-expression network analysis (WGCNA)?
@aliaslam3303
@aliaslam3303 8 месяцев назад
This is very imp
@keepcalm414
@keepcalm414 2 года назад
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 :)
@snehaunni194
@snehaunni194 2 года назад
Sir while uploafing the csv file it always showing disconnected from the server
@birrabukhari3836
@birrabukhari3836 Год назад
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
@asifmolbio
@asifmolbio Год назад
Thanks Bira, glad if it’s helping
@samkhan7536
@samkhan7536 2 года назад
zabardast yar I will watch this full video tonight
@asifmolbio
@asifmolbio 2 года назад
glad if its helpful
@Kaleem.a.q
@Kaleem.a.q 2 года назад
Really impressive informative and expresses your vast knowledge about your field
@hassankarim9451
@hassankarim9451 2 года назад
Thank you, Dr. Asif Bhai, It's really helpful for my work.
@asifmolbio
@asifmolbio 2 года назад
I am glad if it's helpful.
@rubabtalpur9255
@rubabtalpur9255 2 года назад
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
@asifmolbio
@asifmolbio 2 года назад
ok let me check and respond to email
@muhammadrizwan7989
@muhammadrizwan7989 Год назад
God bless you,you lecture is 100%,
@asifmolbio
@asifmolbio Год назад
Thanks stay connected
@muhammadrizwan7989
@muhammadrizwan7989 Год назад
@@asifmolbio i have some question,if possible plz share your wechat or whatsapp,i appricated your hard work
@samkhan7536
@samkhan7536 2 года назад
looking informative for my upcoming samples from china
@samkhan7536
@samkhan7536 2 года назад
thanks for a nice lecture
@asifmolbio
@asifmolbio 2 года назад
Glad you like it
@farhanazhwinmaulana-1298
@farhanazhwinmaulana-1298 2 года назад
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.
@asifmolbio
@asifmolbio 2 года назад
ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-b_042ZbXTwU.html
@drtalhach6071
@drtalhach6071 3 месяца назад
very very helpful.
@asifmolbio
@asifmolbio 3 месяца назад
Glad you like it
@timoac9965
@timoac9965 Год назад
thank you very much. super helpful tool!
@asifmolbio
@asifmolbio Год назад
Glad you like it
@ArshanBukhari
@ArshanBukhari 2 года назад
We’ll explained
@mdnaveedkn
@mdnaveedkn Год назад
Wow 👍👍👍👍🥰🥰🥰🥰🥰
@asifmolbio
@asifmolbio Год назад
Glad you like it
@goodoo6745
@goodoo6745 Год назад
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
@asifmolbio
@asifmolbio Год назад
Glad you like it.
@asifmolbio
@asifmolbio Год назад
ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-rOZda0YWZZs.html
@Beautifullife7189
@Beautifullife7189 Год назад
Thank you sir
@asifmolbio
@asifmolbio Год назад
You are welcome
@MuhammadWaqas-gb5hv
@MuhammadWaqas-gb5hv 9 месяцев назад
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.
@asifmolbio
@asifmolbio 9 месяцев назад
Wslam thanks waqas, i think your specie is not listed your specie genome is sequenced?
@r3v0
@r3v0 2 года назад
Nice and informative videos 👍 Please make a video for tcgadata differential gene expression analysis with r
@asifmolbio
@asifmolbio 2 года назад
Thanks parkash,glad you like it. I have noted down your video topic stay connected
@nouralzayed
@nouralzayed Год назад
❤❤❤❤❤❤❤❤❤
@asifmolbio
@asifmolbio Год назад
❤️
@researchcafee9783
@researchcafee9783 2 года назад
Very informative video.. Thanks Dr Asif. I have one question..How can we convert gene id into gene name?
@asifmolbio
@asifmolbio 2 года назад
which specie or organism you need to change?
@dipenadhikari7967
@dipenadhikari7967 Год назад
sir i find your video very interesting and clear explanation. could you make a video on MA plot.
@asifmolbio
@asifmolbio Год назад
Sure Dipen, will make soon
@ritziroy148
@ritziroy148 7 месяцев назад
Hello, very useful tutorial. May I know whether I can use it for the analysis of mi-RNA nanostring data?
@asifmolbio
@asifmolbio 7 месяцев назад
Yes can be used
@zeeshanpbg
@zeeshanpbg Год назад
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.
@asifmolbio
@asifmolbio Год назад
Thanks you like it, what you mean by authentic sequence?
@SHHR-SH
@SHHR-SH 9 месяцев назад
👏🏼
@asifmolbio
@asifmolbio 9 месяцев назад
Thanks
@SHHR-SH
@SHHR-SH 9 месяцев назад
Could you please share a video about evaluating RNA data and associating it with the disease?
@asifmolbio
@asifmolbio 9 месяцев назад
How to analyze public RNA-seq datasets using iDEP tool ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-BI56K3gYdds.html
@RjAtifAyub
@RjAtifAyub Год назад
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?
@asifmolbio
@asifmolbio Год назад
Must be some errors in formatting, watch video about how to design file for iDEP
@husnainahmad4749
@husnainahmad4749 Год назад
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.
@asifmolbio
@asifmolbio Год назад
ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-rOZda0YWZZs.html
@sohasadeghi689
@sohasadeghi689 8 месяцев назад
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?
@asifmolbio
@asifmolbio 8 месяцев назад
Interactome cannot be prepared using iDEP
@asadriaz3079
@asadriaz3079 2 года назад
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
@asifmolbio
@asifmolbio 2 года назад
Please send your excel DEGs file to me in email
@umarpathologist5863
@umarpathologist5863 Год назад
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?
@asifmolbio
@asifmolbio Год назад
Only mRNAs
@umarpathologist5863
@umarpathologist5863 Год назад
@@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?
@asifmolbio
@asifmolbio Год назад
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.
@jeremiahnwogha8572
@jeremiahnwogha8572 Год назад
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
@asifmolbio
@asifmolbio Год назад
What you mean multiple data ?
@rajithreddy9529
@rajithreddy9529 Год назад
Hi sir,can we write a research paper using data from NCBI by incorporating this tool
@asifmolbio
@asifmolbio Год назад
Off course but clearly mention the source of data in materials and methods section
@rajithreddy9529
@rajithreddy9529 Год назад
@@asifmolbio thanks sir
@hafizmuhammadahmad5314
@hafizmuhammadahmad5314 Год назад
Sir plz make a vedio for creation of cvc file formating
@asifmolbio
@asifmolbio Год назад
ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-hX6IKZkVyRQ.html
@tazuddin3583
@tazuddin3583 2 года назад
Taz Uddin
@mahnoor4499
@mahnoor4499 Год назад
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 ???
@asifmolbio
@asifmolbio Год назад
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.
@TheZubekhan
@TheZubekhan Год назад
it is very informative but Dr. sb it is not best for bigdata analysis...
@asifmolbio
@asifmolbio Год назад
Its ever updating, but still very handy to use
@TheZubekhan
@TheZubekhan Год назад
@@asifmolbio no doubt it’s very easy to use but at then end of uploading data server error
@asifmolbio
@asifmolbio Год назад
Try to perform on only DEGs list
@syedmansoorjan2671
@syedmansoorjan2671 2 года назад
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
@asifmolbio
@asifmolbio 2 года назад
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.
@syedmansoorjan2671
@syedmansoorjan2671 2 года назад
@@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
@asifmolbio
@asifmolbio 2 года назад
Thanks, stay in touch i will make on this topic too very soon InshaAllah
@siphiwemahlangu324
@siphiwemahlangu324 2 года назад
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
@asifmolbio 2 года назад
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.
@siphiwemahlangu324
@siphiwemahlangu324 2 года назад
@@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?
@asifmolbio
@asifmolbio 2 года назад
asifalikalas@foxmail.com
@muhd.shauffianhafiq4140
@muhd.shauffianhafiq4140 Год назад
@@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.
@pakchinalover
@pakchinalover Год назад
We have to mention this website i our manuscript writing?
@asifmolbio
@asifmolbio Год назад
doi.org/10.3390/ijms23147887
@asifmolbio
@asifmolbio Год назад
I have used this website and published an article
@asifmolbio
@asifmolbio Год назад
You can read
@kevine.w.s5828
@kevine.w.s5828 Год назад
👍
@SonuKashyap-gb7vo
@SonuKashyap-gb7vo Год назад
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
@asifmolbio
@asifmolbio Год назад
It shows your technical replicates have significant reads counts, no problem, you can move ahead to follow up analysis and see how PCA works
@karishmaseem6148
@karishmaseem6148 Год назад
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
@asifmolbio
@asifmolbio Год назад
iDEP | how to prepare design file | problems ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-hX6IKZkVyRQ.html
@asifmolbio
@asifmolbio Год назад
Please check this video if its helpful for you
@nikhilchand5329
@nikhilchand5329 Год назад
How can I do idep for wheat data?
@asifmolbio
@asifmolbio Год назад
ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-hX6IKZkVyRQ.html
@asifmolbio
@asifmolbio Год назад
Please watch this video
@abhilipsapanda2420
@abhilipsapanda2420 Год назад
How I recieve data ?? From where??
@asifmolbio
@asifmolbio Год назад
ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-BI56K3gYdds.html
@asifmolbio
@asifmolbio Год назад
Watch this
@abhilipsapanda2420
@abhilipsapanda2420 Год назад
Thank uu sir
@abhilipsapanda2420
@abhilipsapanda2420 Год назад
I want the data of Takifugu rubripes. How can I get that ??? Sir plzz tell me
@asifmolbio
@asifmolbio Год назад
Please watch the video, follow the method if your specie is available
@snehaunni194
@snehaunni194 2 года назад
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
@asifmolbio
@asifmolbio 2 года назад
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
@snehaunni194
@snehaunni194 2 года назад
@@asifmolbio Thank you sir.. But the sequence which trimmed include a portion of my gene of interest.. So what can i do
@snehaunni194
@snehaunni194 2 года назад
@@asifmolbio if possible pls give ur persinal email id sir
@asifmolbio
@asifmolbio 2 года назад
asifalikalas@foxmail.com
@snehaunni194
@snehaunni194 2 года назад
@@asifmolbio thanku sir
@zohaibatif4008
@zohaibatif4008 3 месяца назад
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
@asifmolbio 3 месяца назад
How to interpret the results of proteomics data analysis? Proteomics Data interpretation ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-e8VOm8YFhkA.html
@asifmolbio
@asifmolbio 3 месяца назад
Check out the above video JezakAllah
@zohaibatif4008
@zohaibatif4008 3 месяца назад
@@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
@ImranKhan-yo8hl
@ImranKhan-yo8hl 2 года назад
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
@asifmolbio 2 года назад
How to analyze public RNA-seq datasets using iDEP tool ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-BI56K3gYdds.html
@ImranKhan-yo8hl
@ImranKhan-yo8hl 2 года назад
@@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.
@samkhan7536
@samkhan7536 2 года назад
brother where are you doing job, how I contact you
@asifmolbio
@asifmolbio 2 года назад
I am working as Postdoc in China
@israr2547
@israr2547 2 года назад
ISRARUL HAQUE
@asifmolbio
@asifmolbio 2 года назад
send me your email please
@fifiemap3435
@fifiemap3435 2 года назад
Name:Emmanuel kalumbu
@asifmolbio
@asifmolbio 2 года назад
send me your email please
@nikhilchand5329
@nikhilchand5329 Год назад
Please reply sir please
@asifmolbio
@asifmolbio Год назад
I have sent you a video link it will help you to analyze your specie
@nikhilchand5329
@nikhilchand5329 Год назад
Thanks sir
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