This script is used to process raw ATAC-seq files ready for analysis. Processed files can be opened in the IGV Genome browser to visualise chromatin accessibility.

Download with:

git clone https://github.com/phenotypic/ATACseq-Processor.git

Before running, you must ensure that the reference genome and executable files are located in the the same directory as the script, and that the two ATAC-seq files are located in the ATAC_paired subdirectory. See below:

ATACseq-Processor
│   ├── ATAC_paired
│   │   ├── 30fish-0hpa_S1_L001_R1_00_1.fastq.gz
│   │   └── 30fish-0hpa_S1_L001_R1_00_2.fastq.gz
│   ├── Danio_rerio.GRCz11.dna.toplevel.fa.gz
│   ├── bedClip
│   ├── bedGraphToBigWig
│   └── processor.sh

Start processor.sh from the ATACseq-Processor directory by running:

bash processor.sh

The first thing the script does is generate a quality control report for the two files in the ATAC_paired subdirectory and output it to the Quality_ATAC folder. You can view the reports in a web browser. Use this guide to interpret the results.

Once the script has finished running, open the SPECIES.clipped.sorted.bw file in the IGV Genome browser and load a reference genome to view chromatin accessibility:

• The pipeline used in this script is adapted from this excellent tutorial
• The script should automatically detect the reference genome and ATAC-seq files, as long as they are located in the correct directories. The script will also automatically detect the species shorthand name and the number of CPU cores available
• Building the genome index (step 2) is likely to take a long time as the process is computationally intensive
• Once the script has run and you have saved the SPECIES.clipped.sorted.bw file, you are welcome to delete all of the other files generated as they are no longer needed