trajectory inference

[GreyRockIQ]

Hello Is it possible to run trajectory inference of Asc-seurat with R program created (not Asc-seurat created) rds files? How long can I expect to finish inference for large integrated ads files? Thanks GreyRock

[wendelljpereira]

Hi @GreyRockIQ,

Asc-Seurat expects the rds file to be generated within the application and probably won't work with rds files produced by another approach. We did not test this possibility.

The time for execution of the trajectories will depend on the selected method and the complexity of the dataset (number of cells, expected topology, etc.). The execution will probably be finished in a few minutes when using a small dataset. With a larger dataset, it can take many hours.

The app takes advantage of the models implemented in dynverse (https://dynverse.org/users/2-quick_start/). The web page of dynverse offers guidelines on how to launch a shiny app that helps choose the best model for your data and provides estimates of the number of resources and time of execution for each model.

The models implemented on dynverse rely on Docker images (that Asc-Seurat uses), and their execution will be slower than executing the models directly on your system. If you have an extensive dataset, I suspect it will probably take too long, depending on the model of choice. You are probably better off selecting your model of interest and executing it outside the application.

Cheers, Wendell

[homomedicus]

Please, help!!! I have already tried all the options when working with trajectories. At first I tried to upload my files rds from serat. Then I pre-processed the raw data with the help of your service and again tried to build a trajectory. Nothing works. It just throws the same error - Error during trajectory inference, see output above ↑↑↑. In slingshot mode, everything is fine, but when I try to select one of the dinvers methods, nothing happens, although the docker is running :((

[homomedicus]

[drtm88]

Hi @homomedicus, have you had any luck. I have been having the same issue. @GreyRockIQ were you able to upload and use "non Asc-seurat created rds files" ? Looking forward.