navigating the snRNA-seq code

[davidbmorse]

Hi, and thanks for providing this wonderful resource!

I'm trying to work the the snRNA-seq code and wanted to ask for guidance on how best to proceed.
If I start with the processed snRNA-seq data from the google bucket here, where is the best place to start working this through the code?

Is it best to start with the Jupyter Notebooks here? If so, do you recommend starting at a specific notebook (if not the first)?

Also, is there any reason to look through the Zenodo repository, or is this GitHub sufficient?

Thank you!
David

[herrinca]

Hi David,

Thanks so much for the kind words — really appreciate it!

The h5ad anndata file in the linked bucket includes metadata processed through 05__define-major-clusters-and-dev-trajectories.ipynb, so you should be good to start directly with the 06__ notebook. Also, there’s really no reason to look through Zenodo, it should just point you back to this GitHub repo as it was at the time of publication.

Let me know if you run into any issues or have questions as you go.

Cheers,
Chuck

[davidbmorse]

Hi Chuck,

Thanks so much for the pointer here! That is really helpful, and I'm excited to work though this.

Thanks!
David

[davidbmorse]

Hi Chuck,
I hope you're having a good week.
For the snRNA-seq Notebook 7, cell's 3 and 4 (copied below):

# read in count matrices post nuclei and gene quality control
adata = sc.read( "../data/cleaned_count_matrices.h5ad")

# read in adata post clustering and dev-traj assignment
adata2 = sc.read_h5ad( "../data/post-gaba-wt-dev-traj.h5ad")

Do these two data files correspond with the same processed snRNA-seq data from same google bucket here that I mentioned above (e.g., 'RNA-all_full-counts-and-downsampled-CPM.h5ad' and 'RNA-gaba_full-counts-and-downsampled-CPM.h5ad') respectively? Or are these different files?

Thanks!
David

[herrinca]

Hi David,

Yeah, you are correct, those should be the same files.

Cheers,
Chuck

[davidbmorse]

Thanks so much!
Best,
David