Loom file outdated version for loompy

[daccachejoe]

Hi- I am trying to take Seurat objects and write loom files and use them in loompy but I have run into this error:
Seurat.loom does not appead to be a valid Loom file according to Loom spec version '['2.0.1']'

My loom file version is 0.2.1.9000 but the loom file specifications for loompy as of September 2019 is 3.0.0.

I tried also converting my Seurat objects directly to annData files but that is no longer supported after Seurat v2.4. Have other people run into this issue before? What is the best way to work around this issue?

[jvelghe]

I’m running into this issue as well, but with Seurat v4 objects it seems.

[fentouxungui]

you can use scanpy to read in loom file and then " Creating a Seurat object from AnnData":
https://theislab.github.io/scanpy-in-R/