Reproducible Analysis Notebooks

Hiseq data analysis

• Hiseq2500 Analysis Workflow.

• Hiseq4000 Analysis Workflow.

Novaseq data analysis

• Novaseq 6000 Lane 1 Analysis Workflow.

• Novaseq 6000 Lane 2 Analysis Workflow.

Experimental validation data analysis

• Validation Analysis Notebook Part I.

• Validation Analysis Notebook Part II.

Simulation analysis

• Simulation study.

Downstream analysis

• Effect of Purging on downstream analysis (UMAP) .

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Citation

Farouni, R., Djambazian, H., Ferri, L. E., Ragoussis, J., and Najafabadi, H. S. (2020). Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing. Nature Communications.

The bioRxiv preprint describing the approach can be accessed here.

Contact

R. Farouni and H. S. Najafabadi.

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