phbradley/conga

Question re: GEX cluster assignments

Closed this issue · 3 comments

yls2g13 commented

Great package you've set up here!
I have an integrated 5'GEX single cell RNAseq and TCRseq dataset.

I followed the preprocessing steps in the Seurat_to_Conga.ipynb workflow, then used something like run_conga.py --restart --all
I have my own GEX cluster assignments for my data. How do I incorporate that into my current workflow?

yls2g13 commented

Closing (resolved)

jjs847 commented

hi @yls2g13, do you mind sharing how you did this? Did you use your own UMAP projection or just the labels?

yls2g13 commented

I decided to not use my own UMAP projection and clusters, as it didn't seem very informative. I didn't do this through the run_conga.py utility, but rather through the Seurat_to_Conga.ipynb tutorial and change anything that said adata.obs['clusters_gex'] to match adata.obs['my_own_clusters'].