Creating a Seurat Object from a GEO Dataset 📊

How to create multiple seurat objects from multiple count matrices from GEO and merge them into a single object. #bioinformatics lecture #bioinformaticsforbeginners.
Download the script at github.com/crazyhottommy/comp...
Go to Divingintogeneticsandgenomics.com to learn more!

[@divyamishra2641]

Very clear and informative lecture, thanks Dr. Ming

[@chatomics]

glad it is helpful!

[@jiewang6449]

Thanks a lot for this very informative video!

[@chatomics]

Glad you liked it!

[@mariamendoza5915]

I tried this pipeline but with h5 files and I'm stuck. Do you have a tutorial for that? Please and thank you.

[@annaborchers1756]

Thanks! The files I've downloaded from GEO are in .CEL.gz and .CHP.gz format - how can I use these with your work flow?

[@chatomics]

The CEL file looks like microarray data to me. Are you sure it is single cell data?

[@user-fe7ut1uv5y]

Hello, the tutorial was very informative and i am really thankful for this wonderful video. I am little bit confused. please let me know if we have multiple samples like given in this video then (1) we will first create the seurat object for each sample and then we will merge all these seurat object into one big seurat object before going into quality control, normalization, clustering and UMAP (2) or no, we will first create a seurat object for each samples and then we will perform a quality control, normalization, clustering, and UMAP onto this seurat object. and we will perform the same process for all othe seurat object of other samples and at the end we will merge the seurat?
which one is correct (1) or (2)? looking forward to hearing from you soon

[@chatomics]

I go with 1)

[@mariamendoza5915]

Hello, so most of the datasets that I'm finding come with the 3 files (matrix, features, barcodes), do you have a video on how to automate this? I am currently making individual seurat objects and it takes a long time. Best, Maria

[@chatomics]

Write a function for making a single object. And then use purrr::map to do it for all samples.

[@mariamendoza5915]

@@chatomics I will try this! Thank you so much!

[@seyramm.duphey2248]

Thank you, can you also show how to create a seurat object for spatial transcriptomics please?

[@chatomics]

I have two recent blog posts on it divingintogeneticsandgenomics.rbind.io

[@chatomics]

And if you want a video, I plan to make one in the future

[@seyramm.duphey2248]

Thank you, i will look forward to the video as it is a bit difficult for beginners like myself. Thank youu i will stay tuned@@chatomics

[@georgemichael3724]

Really helpful video, but instead of downloading the entire GEO series, can we download only our relevant data, such as the h5 files? I tried to create the Seurat object using only these files, but when I'm trying to use the 'find variables' function, I get an error indicating that the number of variables is zero.

[@chatomics]

From the GEO ftp site, you can download only the h5 files. I am not sure what’s wrong with your file without detailed information

[@georgemichael3724]

@@chatomicsIs there any chance you could provide me with a recommendation about the Mac that you are using? I'm thinking of changing my current MacBook Air M2

[@mariamendoza5915]

I wanted to try this but I got stuck on step 1. How do you download with FTP?

[@chatomics]

Follow this github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/04_create_seurat_object_from_GEO.Rmd

[@thethingsilove902]

@@chatomicsThank you! I will give it a try