Mammoth Cup Bioinformatics

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library_books Completed

RefRead

Verified 2m ago

sync

stars Processing

STAR Align

radio_button_unchecked Pending

Bead Calling

Waiting for input...

bar_chart Pending

Quantification

Queued

hub Pending

Clustering

Queued

Sequencing Saturation

Real-time Read Depth

trending_up 82.4%

Mitochondrial Content %

Quality Control Metric

check_circle Stable (5%)

S-01

S-02

S-03

S-04

vpn_key

Achievement Unlocked

Gene Key Found! +500 pts

terminal Optimization Script

main.py

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import scanpy as sc
import numpy as np

# Configure settings for visual style
sc.settings.verbosity = 3
sc.logging.print_header()
sc.settings.set_figure_params(
    dpi=80, 
    facecolor='white'
)

# Load dataset from BloomAI Repo
adata = sc.read_10x_mtx(
    './data/mammoth_v2/',
    var_names='gene_symbols',
    cache=True
)

# Optimize STAR alignment params
def optimize_alignment(adata):
    sc.pp.filter_cells(
        adata, 
        min_genes=200
    )
    sc.pp.filter_genes(
        adata, 
        min_cells=3
    )
    
    return adata.copy()

adata = optimize_alignment(adata)

Console Output

> Initializing environment...

> Connection established: ws://mammoth-node-04

> Loading reference genome hg38...

> [STAR] Started mapping job #88219

> [INFO] Processing batch 1 of 4...

> _