Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners
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- čas přidán 19. 11. 2021
- #bioinformagician #bioinformatics #genomics #beginners #tutorial #howto #omics #research #biology #ncbi #GEO #rnaseq #ngs
This is a basic tutorial to download gene expression (RNA-Seq) data from NCBI GEO. Hope you found this tutorial helpful.
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Email: khushbu_p@hotmail.com
Your work is not just helpful it is precious. Please keep posting more awesome content!
Hello! I'm new here and just wanna say: Please, don't stop posting these videos! I'm Brazilian but now I'm in the USA doing part of my Ph.D. research in bioinformatics. It has been really challenging once I did nothing in this field before, and I'm just starting to understand this world of bioinformatics. It has been difficult in many aspects because I'm learning from the beginning and still struggling with the language (in fact, the languages, the computational, and the English LOL) and the concepts. This channel has been so helpful because your explanations are given in an understandable way. Thank you very much.
I really appreciate your kind words. Thank you very much :)
@@Bioinformagician I like your way of explaining 😻
I am also a newly enrolled student from India doing PhD in Bioinformatics its been only two weeks since i joined its very difficult at the moment since my background has always been of purely biotechnology but maam's videos has helped to clear many of my concepts till now and she teaches very nicely ! learning through her videos is a great relief and I hope you are in a much better position now !
I appreciate your videos so much. It helps me refresh back the things I've forgotten from my undergraduate studies
Thank you so much for this! Your videos are wonderfully informative and I look forward to watching all of these! Out of all the bioinformatics videos I've come across while trying to learn all of this for my summer program, you have been the most simple, thorough, and engaging! Thank you for the work you have done to support so many people.
I'm so glad!
Going to use this to study Bioinformatics during my gap year before I apply to master programs in Bioinformatics; many thanks for creating these videos!
Your channel is the best youtube channel for bioinformatics that I have ever taken as reference for my study.
Man, you’re life saver! Thank you so much
Omg! I have used NCBI for so long and never knew the existence of so much data. So cool!! Thank you!
I am glad to know this was informative ❤️
Your videos are very helpful. Keep posting!
Awesome work! I am in a similar situation als Valesca and your work is saving me lots of time!
Gosh! Your video series are SO HELPFUL! Thankyou so much for your wonderful contents and please make more videos on RNA-Seq for beginners like me!
Excellent description of GEO
Thank you for the tutorial. It is a good way to understand basic principles of bioinformatics. Thanks again.
My God, you cannot imagine how useful your videos are!!! Thank you so much for creating this! Liebe Gruße von München! 🥨
Very helpful, don't stop posting, please. Thank you
YOU ARE A LITERAL GOD! MASTER PATEL! JUST KEEP POSTING VIDEOS
Your videos will help me do my thesis :)
It was very informative! Thanks deeply!
Excellent video! It has been very helpful for my work. Thank you so much!
Awesome channel and very informal videos. Thank you and looking forward to new videos. Keep up the good work!
Thank you, I am glad you find my videos helpful! 🤗
Beautiful lesson, thank you (from Italy).
Hi, I am new to this channel. I really appreciate the way you have explained the topic. Thanks
U have made a very good video and explained each step nicely...thanks a ton for such lovely tutorial for beginners..
Thank you for this video !!
You are my secondary guide.
You have no idea how noble a job you are doing helping people like me. I pray for your success and good health ❤ much love
Thank you for this video! It's very helpful :)
Nice work, very helpful
Thank you. It was a great help
Your videos are not only interesting but easy to follow . your presentation is fanny and you are synpatic
Thank you very much for the content. It has been very helpful
Awesome
It was awesome video, thanks a lot magician 🙂
Peaceful learning 🎉
very helpful, thx.
THATS GREAT
You are amazing..
Thank you so much😊
Hello Khushboo - wonderful work you are doing here! Is gunzip a package you downloaded on R?
Hey, I am passionate about Bioinformatics and I found your videos really very enthusiastic ❤ keep posting videos like that also on some basics of Bioinformatics.
And may I know how can I find the GSM IDs?
Hello and thank for all you content! I'm very grateful. One question, now in 2023, are rna-seq the new standard for gene expression profiling or microarrays have still their share in new studies?
thank you
Great work. Loved your channel. can you please create a playlist for RNA-seq analysis starting from the preprocessing steps to the use of the data to find DGE?
Good idea, I will work on creating such a playlist. Thanks for the suggestion!
Thanks for posting this video! I have one question, if I want to search the RNA-seq studies for knockdown/knockout specific genes (e.g. TP53) in GEO, what should I do?
Hello!! Thanks a lot for your videos. Your channel helps me a lot. I'm starting in the world of bioinformatics, and I've been mining information in many places, but your videos are some of the most didactic I've found. Please keep teaching, you have a great didactic.
I take the opportunity to ask a question. In your video, you commented that it is not ideal to open the counting tables in excel because it unconfigures (in fact, I already have this issue). Which program would you recommend using, and one that is easy to edit (for example, allows you to filter columns)?
Thanks
I appreciate your kind words. In order to deal with count tables, one can use a functional programming language like R, Python or Perl that provides data structures like datatables/dataframes which will provide the right functions and methods to manipulate (like filter columns) your data.
😍
Your Videos are great and helps me every time when I looks for queries related to bioinformatics analysis!! I would like to ask one question that, is it necessary that we should only choose the RNA-seq GEO dataset with .CSV extension or can we choose .TXT. Does both of them contain similar information? As my analysis is to generate counts data from the desired GEO dataset through SRA analysis. Your guidance will be greatly appreciated. Thank you.
I wish I could give you a 1K like. This tutorial was very informative and delivered in an easy way. You mentioned excel is not a choice tool to open such data what ideal tool do you recommend otherwise.
Use R
Hi, can you make a tutorial video on how to analysis RADSeq data using R
Hello, it's great video, thank you. Will you show how to analyze RNA-Seq data in your next videos?
Hi, I am glad you found my video helpful! I am planning to create more videos to perform various analyses on RNA-Seq data. I uploaded a video yesterday that shows how to perform data manipulation on the same data in R using dplyr (czcams.com/video/4CkRXGWmAbU/video.html), if that is of interest, make sure you take a look!
@@Bioinformagician hi thank you for this informative videos.
Can we extract the expression data for few genes using GEO database.
Hi.. Thank you for your videos. Can you please create a playlist that beginers who have no experience i NGS can learn and follow to conduct NGS data analysis and research? Like step by step. What shall be the first step and following steps.. It will be convinient for beginers to follow.
Hi i am new in bioinformatics and watching your video for the first time which terminal you tell to extract csv.gz file to csv file?
Hi , i am new to bioinformatics what i wanted to know what is the difference between gene expression data and proteomics data. In proteomics data, i have encountered fields like REP-1 , REp-2..what do they actually represent
What is the best tool for opening these types of data files in Mac?
Hello. I am newbie in using R software and performing scRNA analysis. I an very thankful and have found your videos very helpful. Now I have to work on my data files in .txt.gz files (GEO). Can you help me in this regard as using .tx.gz file has a different display when import into R :(
Hi, Thanks a lot for your wonderful videos. Would you please make videos on "generating different types of graphs and plots in R" in the easiest way?
Noted! Thank you!
Very good video. But I was wondering how could we download the processed short read scRNA seq data from GEO and NOT the metadata?
Hello thank you for the video. I really love your effort.
I have a question. How do we recognise as to which dataset to choose from? Do we always use GEO for dowloading RNA-Seq data?
Your criteria to select a dataset can depend on so many things like the experimental design, animal model, disease studied..etc.
Regarding the RNA-Seq data repositories, there are other sources as well like Expression Atlas from EBI (www.ebi.ac.uk/gxa/home/) where you can get RNA-Seq data. There are also various publications where RNA-Seq data is generated and studied.
hello!! thank you so much for this
I am also interested in learning how to search wisely. I am looking for data sets to pull down for my students to analyze.
Usually, my selection for datasets depends on the associated publication. If you are looking for some breast cancer datasets, it might be helpful to look for papers that have conducted comparative studies using breast cancer data. In addition, I also prefer to look for papers published in high-impact factor journals, these papers have gone through a rigorous review process, which adds more confidence in the data and findings associated with the paper. Another measure would be to look at the number of times the associated publication has been cited.
The next consideration while choosing a dataset is the expression unit, as you mentioned more often it so happens that datasets are in different units. In such a case, either you can use counts and normalize them to the same units or get the raw data (RNA-Seq reads) and process data using standardized pipelines and quantify gene expression to the same units, I prefer the latter.
Lastly, there are large public data repositories like the TCGA data portal (portal.gdc.cancer.gov/) which hosts a lot of data available for anyone to access. You will find a lot of breast cancer datasets (in addition to many other histologies) and data is available in various units like counts, TPM, FPKM/RPKM. A plus of using the TCGA portal is it collects raw data from many cancer projects and processes them using standardized pipelines which makes comparison across different sources/projects sensible and valid.
Hope this helps! :)
@@Bioinformagician wah! thank you so much for this!! your entire channel is a lifesaver to my undergrad thesis!!! will surely add you to my dedication :
@@Bioinformagician And just to share, I was planning to use series from GEO as my study/training cohort, and TCGA dataset for my validation cohort, but I am honestly still confused on how a validation cohort works, but I will hopefully figure it out along the way!
Dear madam, is it possible to analyse the rna sea data from various experiments like meta analysis
Yes, you can perform meta-analysis using various RNA-Seq datasets. Check out this package in R to perform such analysis - www.metafor-project.org/doku.php/metafor
@@Bioinformagician madam, can't we do with deseq2
Hello. Thank you very much for this video. Can you please make a video about automatic Cell type annotation in clustered data using R? Thank you...
Thank you for the suggestion, will surely think about making a video on this soon :)
So if Excel is not the right choice, which program should we used
Hello,
I have a question, is it possible to combine multiple geo datasets with different platforms and experiment types? I have 5 GEO datasets in which two of them is expression profiling by high throughput sequencing and the rest is expression profiling by array, noting that each one has different platform?
You cannot combine datasets from microarray and RNA-Seq and normalize them and make comparisons between them as they are completely different technologies. Having said that, you can process them separately, compare the results and/or perform meta-analysis on the results.
Is the terminal similar to commands in windows?
Hello, nice video
I apologize
what hardware do you recomend to use?
My currently setup
i7-6000K
8 GiB RAM
It totally depends on what data you will be dealing with, what analysis you plan to perform, and the tools you intend to use. Your current configuration is good enough to be dealing with smaller data.
@@Bioinformagicianvery
Thank you, useful comment
Do you recommand using x3dna?
@@pentosa I have close to no experience in structural bioinformatics. Unfortunately I cannot provide any recommendations for those tools. Sorry!
Is bioinformatics has future demand
Please make a lecture regarding wgcna analysis.
It's in my pipeline. Will soon be making a video covering this topic. Thanks!
thank you so much i i have one dout I am get this error
Error in gse[[1]] : this S4 class is not subsettable
what should I do for data
Dear mam, please upload a video n metabolomics analysis using pRocessomics R package, please
Hi Khushbu . Can u plz make a video regarding STAR alignment. Also please try n make videos for windows user too. As I was able to configure sra tool kit but couldn’t go further..
Thank you
I surely plan on creating a video on RNA-Seq pipeline, from alignment to gene quantification step. Since I have a mac, unfortunately I cannot demonstrate workflows in a windows system. However, if you encounter errors, do post them. There are a lot of windows users, someone will be able to help you.
Hi sister, I am Ph. d student but new in Bioinformatics. i have to write a chapter of my thesis as protein enrichment analysis. there is no one to guide me. CZcams is only teacher for me.
I want to study a protein in relation to kidney disease, its pathways, and networks etc.
Please make a video for a beginner who dont know anything and just need to start.
What are things I need to know first, what data I will need to extract first or whatever you know need to know first thing to start this.
I need to know steps from wher to start and what to search for. there are many good videos but everyone discuss directly think that we know everything. But we need to even know such small things like unique IDs etc.
Hi, thank you for the video! I tried to apply your video on microarray data (GSE65645) but the extension of the folder differs (.tar) and when I unzip the compressed folder I get a bunch of txt files. Can you give a hint how to analyze this type of information, or can you please suggest any website or source where I can learn how to analyze them in R studio?
I looked up this record on NCBI GEO and it seems the supplementary file (ending in _RAW.tar) contains data about signal intensities from scanned images processed using Feature Extraction software.
I am assuming you are interested in getting the normalized and log2-transformed expression data for all samples. You can get that by executing the following commands in RStudio:
library(GEOquery)
geo_id
Very informative video. Can you make some video on metatranscriptomics
@@tulikabhardwaj484 I will surely think about making a video on it soon :)
@@Bioinformagician thanks a lot. it's a helpful tutorial. However the object, data, obtained by this method, i.e. data
@@yeunglee2565 I am not sure if I understand, can you please explain what do you mean by different? Do you mean you don't get the expression data when you run this command?
Thanks, great video
i have a quistion: are there other organizations to get patients data to do a research? because i am facing a challenges to get data from hospitals. thank you
There are a lot of open source repositories which make de-identified data from patients accessible to the public. Check out - portal.gdc.cancer.gov/, xenabrowser.net/datapages/, www.cbioportal.org/ and lastly the publications that generate data serve as the best source for data.
Hello! I want to ask, do I have to carry out batch effect removal from scRNA seq data download from GEO NCBI?
If you observe batch effects in your data, then yes, you should correct for them.
Can u plz make a tutorial for Hi -C DATA ANALYSIS
Thanks for the suggestion. I'll surely think about making a video covering this topic.
does Terminal work on windows 11 ?
Hello , I want to work with GSE dataset from GEO base i.e. GSE70970. I want to download this data from GEO to R. Installation of BiocManager was smooth. But after that I an wondering which Bioconductor packages I need to install to operate GSE dataset. BiocManager::install("limma") basically this is the code I am trying to run, but failed. Please share your suggestions.
Can you share the exact error you see when you try to install limma?
please also mark videos as Lecture 1 lecture 2 so that we know which video need to see first.
Most videos do not follow any predetermined order. The ones that are intended to be followed one after the other has been named as PART 1 or PART 2.
Hi.. Thanks for the videos. I want to know that can someone with no knowledge and experience of R perform RNA seq analysis in R, by watching your videos? Please answer me. As I'm planning to take up a project on RNA SEQ Analysis.
There will be a steep learning curve. With perseverance and decent googling skills, it is doable.
Can you explain what are the files in the download family?
There is a SOFT file, an MINMAL file and a Series matrix file.
If you or someone here could explain what they are that would be great
what about tpm datasets?? i followed your video. you used same dataset as this video and i used the tpm data set then i saw there is no matching things happening help me out please sister
If in overall design, it is not mentioned "Original reads of RNA sequencing data were normalized as FPKM data" then what else... any suggestion or opinion?
If no information is provided about the kind of normalization performed, you could either reach out to the authors who have submitted this data or you could see if they have provided raw data in supplementary files. If they have, you can process and normalize it for your downstream analysis.
@@Bioinformagician Do you plan on making such tutorial on how to normalize data in R..
@@syedmansoorjan2671 Yes, I plan to talk about different methods of normalization in a future video.
@@Bioinformagician That's cool, I expect as you did in previous videos, from basic to advanced..
Hello, In your video you mentioned about opening a .gz file by unzipping it. In my case I have a GEO database "GSE237622_RAW.tar". When I extract this using 7 zip, it results in an tar.gz file. How to work with this file format to get a final csv version of this dataset. Thank you
linuxize.com/post/how-to-extract-unzip-tar-gz-file/#:~:text=Conclusion,followed%20by%20the%20archive%20name.
Your videos are so simple and magestic but the only problem is the sequencing of video is not done so its very hard to find which video is after what. EG: Its not easy to find which video is corresponding to it. If you can name them like 1, 2, 3 it would be fantastic
Thank you for the suggestion. I will ensure to put numbering in my video titles when they are in sequencing order. Most videos on my channel do not follow any pre-determined order.
Hi, I want to download fastq files for RNASEQ data, please help how to download
What to do when the dataset has no description about normalization , written only dataset was normalized. please reply maam.
You could refer to the associated publication and read methods section to see if they have mentioned what normalization was performed. If not, you might have to contact the authors for that information.
@@Bioinformagician ok, thank you, Maam.
Hello Maam, I am currently pursuing PhD in bioinformatics. I want to learn microarray and gene expression analysis in R.Could you please teach me online , I am ready to pay course fee.
Unfortunately I do not provide tutoring. I intend to share my learnings via my videos. Happy to answer any questions you may have :)
i cant convert .CEL format to . csv , plz anyone help.
.CEL files are raw files from microarray data. You will need to perform an RMA normalization on raw data present in .CEL files. Here's a nice step-by-step tutorial: felixfan.github.io/RMA-Normalization-Microarray/
@@Bioinformagician thank you so much,
Hello! thanks for the video. I am PhD student (Cambridge) not very much familiar with data mining but I am looking to extract gene expression from multiple RNA-seq database (Meta-analysis). Would you be able to help me with this? Can you provide your Email-id for future communication?
Thanks!
Happy to help to the best of my knowledge! You can find my email in the description section of every video :)
Hindi me dala kro video
dont copy the lacture of Dr Naveed hhhhhh