Welcome to genPALS workshop 2021
17 September 2021
Time | Topic | Presenter |
11AM – 11:30 AM | Welcome and introduction Single-cell genomics overview | Sam Morabito |
11:30 AM – 12:00 PM | Experimental overview of scRNA-seq | Liz Rebboah |
12PM – 1PM | Lunch | Mendocino Farms |
1PM – 2PM | Pre-processing raw sequencing data | Fairlie Reese |
What is GenPALS?
Bioinformatic methods
Your data
You
genPALS
How am I supposed to figure out how to analyze my data???
How am I supposed to figure out how to analyze my data???
What will I learn by attending genPALS throughout Fall 2021?
Your first single-cell genomics analysis
a story in pictures
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single-cell genomics starter pack
Why should I listen to you? I can just copy and paste from a tutorial, right?
snRNA-seq analysis of the prefrontal cortex of 32 individuals
A real single-cell dataset vs the PBMC tutorial dataset
Re-processing the Zhou et al dataset using the scanpy tutorial code
Inspect quality of all 32 samples
Data normalization and scaling
scanpy.pp.log1p(data)
scanpy.pp.scale(data)
The curse of dimensionality
Feature Selection & Principal Component Analysis (PCA)
scanpy.pp.highly_variable_genes(data) scanpy.tl.pca(data)
Feature Selection & Principal Component Analysis (PCA)
33k genes
50 Principal Components (PCs)
Highly variable genes
Visualizing the top Principal Components
33k genes
50 Principal Components (PCs)
Highly variable genes
Non-linear dimensionality reduction (UMAP, tSNE, etc)
scanpy.pp.neighbors(data, n_pcs=30) scanpy.tl.umap(data)
UMAP colored by AD Diagnosis of patient samples
UMAP colored by Sample ID
UMAP colored by cell-type marker genes
Grouping cells into clusters
scanpy.tl.leiden(data)
UMAP colored by cluster assignment
UMAP colored by sequencing batch
UMAP colored by log(total UMI counts)
UMAP colored by percent mitochondrial reads
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I don’t know what’s wrong with my data…
batch effects?
ambient RNA?
how many clusters???
doublets?
mitochondrial clusters?
UMAP or t-SNE?
what should I filter?
compare to published data?
cross-species analysis?
when do I stop analyzing?
Topics for Fall 2021 genPALS series
Join our Slack workspace!
And go to the workshops_2021 channel!