README.md

cellranger-atac-hg19

Cell Ranger ATAC v2 no longer provides the hg19 reference package out of the box. This is the instructions to create a hg19 reference package for Cell Ranger ATAC v2.

Prerequisites

• The Cell Ranger ATAC executables/binaries should be accessible from anywhere.
• Python 3

Create a Python virtual environment and install the dependencies:

pip install -r requirements.txt

Build

Download FASTA, GTF, and transcription factor motif position-weight matrices in JASPAR format:

./download.sh

Fix the chromosome names (e.g. chr1 --> 1, chrX --> X, chrM --> MT, ...):

python fix_chr_names.py

Run the Cell Ranger's mkref command:

./mkref.sh

Final Directory Structure

.
├── refdata-cellranger-atac-hg19-Gencode-v28
│   ├── fasta
│   │   ├── genome.fa
│   │   ├── genome.fa.amb
│   │   ├── genome.fa.ann
│   │   ├── genome.fa.bwt
│   │   ├── genome.fa.fai
│   │   ├── genome.fa.pac
│   │   └── genome.fa.sa
│   ├── genes
│   │   └── genes.gtf.gz
│   ├── regions
│   │   ├── motifs.pfm
│   │   ├── transcripts.bed
│   │   └── tss.bed
│   └── reference.json
├── JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.txt
├── README.md
├── download.sh
├── fix_chr_names.py
├── gencode.v28lift37.basic.annotation.fixed.gtf
├── gencode.v28lift37.basic.annotation.gtf
├── hg19-Gencode_v28.config
├── hs37d5.fa
└── mkref.sh