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biomystery / snATAC_pipeline_scanpy_based

A single-cell ATAC pipeline based on scanpy and clustering on most variable genomic bins. Originated from Josh@Kyle's lab.
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jupyter-notebook pipeline python python3 r

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snATAC pipeline

** Steps

  1. Run 10x cellranger
  2. Run preprocessing pipeline
  3. Run Run_prefilter.py to get thresholds
  4. Run Run_jupyter.py to do initial clustering
  5. Run Run_scrublet.py to get scrublet doublet score
  6. Run Run_merge.py to merge samples

** Improvements

  1. Get cut_freq_matrix for prom x cells
  2. Group frag/reads for (cells in) clusters, then call peaks
  3. Merge frag/reads