DATA GENERATION STEPS:

1 - Download PRO-seq read counts fastq files from SRA. 
    * GEO Accession: GSE144786
    * human reference genome hg19
    * Control Sample ID: SRR11024616
    * Auxin Treated Sample ID: SRR11024617

2 - Process and align PRO-seq fastq single-end (SE) read data using proseq2.0 software to get bigwig files
    * https://github.com/Danko-Lab/proseq2.0
    * Refer to SRA experiment information for adapter sequences used and spike in scaling factor information
        - https://www.ncbi.nlm.nih.gov/sra/SRX7677755
        - https://www.ncbi.nlm.nih.gov/sra/SRX7677756

3 - Generate GRanges objects for pause regions and gene body regions
    * Used Ensembl version 75 to download hg19 GTF annotations file
    * Import GTF file into GRanges object
    * Extract pause regions and gene body regions into separate GRanges objects

4 - Subset example data
    * The "*_subset.bw" bigwig files included in inst/extdata/ are
      restricted to chr21:41,100,000-46,700,000 (hg19), covering 47 of
      the original 95 genes in granges_for_read_counting_DLD1_chr21.RData
    * bw_pause_filtered and bw_gb_filtered in
      granges_for_read_counting_DLD1_chr21.RData were filtered to the
      same 47 genes, keeping only genes whose pause and gene-body
      ranges fall entirely within that region
