- Align to the reference genome (Bowtie2).
- Remove duplicate reads (Sambamba).
- Generate genome browser tracks.
- Call peaks (MACS and HMMRATAC).
Set up a new analysis (common across all routes). If running for the first time, check the detailed usage instructions for an explanation of every step.
cd <project dir> git clone --depth 1 https://github.com/igordot/sns sns/generate-settings <genome> sns/gather-fastqs <fastq dir>
Check for potential problems.
grep "ERROR:" logs-sbatch/*
BAM-DD: Deduplicated BAM files. Can be used for additional analysis.
BIGWIG: BigWig files normalized to the total number of reads. Can be used for visual inspection of peaks.
summary-combined.atac.csv: Summary table that includes the number of reads, alignment rate, and fraction of PCR duplicates.
summary.qc-fragment-sizes.png: Distribution of fragment sizes.