search

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
381 stars 85 forks source link

CellBender from StarSolo output #962

Closed davidsanin closed 8 months ago

davidsanin commented 8 months ago

Hey All! I wanted to try out this de-noising tool that was published in 2023: https://cellbender.readthedocs.io/en/latest/index.html It is built to work from the unfiltered HDF5 file that cellRanger generates. If I wanted to recreate that file, what would be a good starting point? Currently I am considering saving the "raw" merged Seurat object as an .h5 and trying that out. I'd appreciate any suggestions!!

davidsanin commented 8 months ago

Ignore me! I can just run it with the StarSolo "X.Solo.out/Gene/raw/" outputs!