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YosefLab / Compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
BSD 3-Clause "New" or "Revised" License
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Can we use “extdata/RECON2/reaction_metadata.csv” for mice's compass analysis？ #54

Closed 1213812138zqc closed 2 years ago

1213812138zqc commented 2 years ago

Currently, we are analyzing our scRNA-seq data obtained from the mice through Compass platform. I want to ask if we can use “extdata/RECON2/reaction_metadata.csv”(suitable for human in your analysis) to perform downstream analysis.

schel337 commented 2 years ago

Yes, in our analysis the Th17 cells actually come from mice and we used that metadata for analysis of the cells. The use of Recon2 is a limitation of the study, among those we list in the Cell paper, though we have been looking into adding other models to Compass. I will add some clarifications to our online documentation.

The species parameter on the command line determines whether to look for human or mouse genes, if that helps clarify things. It does not change the model.

1213812138zqc commented 2 years ago

Thanks for detailed explanations

allonw commented 2 years ago

Thanks Brandon for the answer. I'll just add that it's common in FBA studies to use Recon also for mouse data because of its magnitude and breadth and despite the differences that exist between murine and human metabolism.