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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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converting loom files to seurat objects #273

Closed kwglam closed 3 years ago

kwglam commented 3 years ago

Thanks for creating and maintaining the zUMIs!!

I have successfully run my Smart-seq3 data using zUMIs. I am trying to do the downstream analysis by converting the loom files generated in the zUMIs_output folder into Seurat objects. However, when I use as.Seurat() function to convert my loom files, it came up with an error message: "Error in x$version() : attempt to apply non-function". To my understanding, you use loomR package to convert rds files to loom files. Do you know if the problem is caused by the version of loomR? I am wondering if you have ever come across similar problems in converting loom files generated by the zUMIs to Seurat objects. Many thanks!

cziegenhain commented 3 years ago

If you're working in R / with Seurat and the loom files are iffy, I suggest to just take the count table from zUMIs main output file (zUMIs_output/expression/*.dgecounts.rds) https://github.com/sdparekh/zUMIs/wiki/Output#structure-of-the-output-dgecounts-object-in-project_namedgecountsrds

kwglam commented 3 years ago

Thanks, Christoph. I will use the rds file instead.