Hello ! I have downloaded data from GEO bit there is not the 10X format (features.tsv, barcode.tsv, matrix.mtx), there is only cloupe file, is it possible to create the 10x format files from cloupe ? how can I do ? with R if possible please (I would like to create a seurat object) Thanks for you answers
1 answer
As far as I know it should not be possible.
You can convert a seurat object to cloupe format, but not the inverse. This might change in the future (see here) . It is very strange that the authors uploaded in GEO only the cloupe file. Is the paper still in review? You should contact them and ask for the h5 files of the samples.
If the h5 are available then you simply need to follow one the tutorials available on seurat's website. Based on the nature of the data and the type of analysis you are trying to do you should be able to find the right one, but if you don't know where to start, then pbmc 3k guided tutorial is a good start.
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