Entering edit mode
2.0 years ago
Muny
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0
My question is pretty straightforward although I couldn't find a definitive answer online. I am interested in analyzing all of the human samples in a single experiment on GEO. Normally I have loaded the supplementary files that include counts, barcodes and features into a Seurat object but does that include every sample? Or would I have to download the RAW.tar file and combine them manually?
Each set of barcodes+features+matrix is a separate single cell dataset, so I don't see how you can read many of them into a single Seurat object. You may have to read them into separate objects and merge them if the merging operation makes sense.
I think the tar file is just some of those individual files as a tarball.
Thank you for the response. I understand that I would need to merge each dataset into a separate Seurat object, what I am wondering is if the supplementary files for a GSE would include all samples. Typically I find the .mtx, barcodes and features for individual GSM files. But would a GSE of .mtx, barcodes and features as shown above include all the samples in the experiment? I have found that the GSE file size of the human .mtx, barcodes and features are comparable to the sum of the individual GSM files, I just wanted to be sure.
That's a good question. You may want to download a couple of GSM barcodes files and the GSE barcodes file and examine the overlap.