Process Query Datasets

prep_data/prepare_query

• Software needed

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

  • gunzip

• load input files in prepare_query.sh

  • reference peak file peaks.bed

  • Frag_path path to fragments.tsv.gz

  • Barcode_path path to barcodes.tsv

  • hg38.chrom.sizes.txt within the prepare_query folder

• command to process query data

bash prepare_query.sh

This command will prepare the query data based on the following steps:

• 1. prepare peak-cell matrix file

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

• 3. prepare reference atlas h5ad file for scATAnno