ATAC-seq pipeline Release 2.0

Version 2.0 - November 2019:

Included TF footprinting, optional discarding of blacklisted genomic regions, motif analysis

Updated summary statistics incorporating support for ATAQV package (https://github.com/ParkerLab/ataqv)

Discarded R package ATACseqQC (https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html) and corresponding operations, mainly due to its time complexity and reliability issues.

First Release

ATAC-seq processing pipeline, supporting either fastq or bam files, and single or paired end reads.
Alignment statistics, quality thresholding of reads, and de-duplication is performed.
Peak calling using MACS2 is done.
QC metrics suggested in Greenleaf et al 2013 are also implemented, and the package ATACseqQC is also integrated for this purpose.
UCSC compatible tracks are also created for visualization.