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6e124c9 · Jun 17, 2020

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T1D_snATAC_pipeline

README.md

Instructions

Run the snATAC_pipeline_CB.py (for combinatorial indexing single cell ATAC-seq) or snATAC_pipeline_10X.py (for droplet-based 10X single cell ATAC-seq) pipeline to generate input matrices for clustering.

Use the T1D_merged_snATAC.ipynb notebook using the input matrices to cluster cells.

Requirements

Software packages

R
trim_galore
bwa
samtools
bedtools
picard
macs2

python3 packages

numpy
pandas
scipy
matplotlib
seaborn
pysam
rpy2
scanpy
anndata

R packages

Matrix
harmony