ATAC-seq

ATAC-seq pipeline for snakemake

Steps:

1. fastqc - to check quality on fastq.gz files

2. trim_galore_pairedend - trim nextera adapters

3. bwa_mem_pairedend - align to hg19

4. samtobam - convert sam to bam file

5. mapped_bam - remove unmapped reads (aka. reads that did not align to reference genome)

6. sort_bam - sort reads by chromosome and region

7. index_bam_bai - create index

8. fastqc_bam - check quality of bam files

9. macs2 - call peaks

10. macs2_header - add header for compatibility with DESeq

11. ATACseq_Rcode - run DESeq analysis and build plots (incomplete)