Prepare Reference Atlas

How to Build a Reference

• Code used for reference budiling

prep_data/scATAnno-reference-building-example

• Software needed

  • please install https://github.com/AllenWLynch/QuickATAC

  • MACS2 if need to call peaks

  • gunzip

• load input files in build_reference.sh

  • Frag_path path to fragments.tsv.gz

  • Barcode_path path to barcodes.tsv

  • hg38.chrom.sizes.txt within the reference buidling folder hg38.chrom.sizes.txt

• command to create the reference

bash build_reference.sh

This command will build reference based on the following steps:

• 1. call peaks using MACS2 from fragment file

• 2. prepare peak-cell matrix file

• 3. construct peak-cell matrix for reference atlas using QuickATAC

• 4. prepare reference atlas h5ad file for scATAnno

• 5. (optional) Create reference low-dimensional spectral embedding for futher use

Healthy Adult Reference Atlas

• Select deep-sequenced 100K adult cells

• Select adult specific peaks (~ 890K peaks)

• Downloaded Healthy Adult Reference atlas

  

  Perform dimensionality reduction using spectral embedding, visualize annotation on UMAP

PBMC Reference Atlas

• Select 39441 PBMC cells

• Generate 196K peaks by MACS2 Peak-Calling

• Downloaded PBMC atlas

  

  Perform dimensionality reduction using spectral embedding, visualize annotation on UMAP

BCC TIL Reference Atlas

• Select 22008 TIL cells

• Generate 340K peaks by MACS2 Peak-Calling

• Downloaded TIL atlas

  

  Perform dimensionality reduction using spectral embedding, visualize annotation on UMAP