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euxhenh / cellar

Interactive software tool for the assignment of cell types in single-cell studies.
https://cellar.cmu.hubmapconsortium.org/app/cellar
MIT License
31 stars 5 forks source link

Upload File #7

Open elissonlopes opened 1 year ago

elissonlopes commented 1 year ago

Hello.

Great Tool! I could run Cellar in one of my samples, 10x data, worked great. I still don't know the better way to upload the whole batch as one file to be analyzed. Can you give a help with it?

euxhenh commented 1 year ago

Hi,

Cellar currently doesn't support concatenation of AnnData's, but you can easily do this yourself locally by using the AnnData.concat function. See examples here.

You can then upload the combined file to Cellar.

elissonlopes commented 1 year ago

I got another problem.

*The first part was solved using: library(SeuratDisk)

SaveH5Seurat(pbmc, filename = "./mfg2.h5Seurat") Convert("./mfg2.h5Seurat", dest = "h5ad")

*And now: When I tried to submit .h5ad file to Cellar I got a message: Error encountered while reading file. Maybe the file is not formatted properly, or invalid entries were found.

Does Cellar has a limit size for files? Or do you know any possible reason to have this error?

euxhenh commented 1 year ago

h5Seurat is a different file format than h5ad and Cellar will not recognize it. See if you can use the H5SeuratToH5AD package to convert it [source].

elissonlopes commented 1 year ago

I convert again using this line above: Convert("./mfg2.h5Seurat", dest = "h5ad") Its a H5AD file. I also tested using csv file. I suppose it would be something with the file size? Is there a limit in cellar?

euxhenh commented 1 year ago

There is a limit of 2gb. Before uploading to Cellar, you could try loading the file locally and debug any errors there. If using Python, install the anndata package and load the file with anndata.read_h5ad('filename.h5ad').