This section aims to reanalyze the data retrived from a publication by Griffith et al. (2015).

TODO:

• retrieve and extract data: reference genome (.fasta), reads (.fastq), annotation file (.gff)
• generate reference index (.idx)
• align reads to reference (.sam)
• convert SAM to BAM (.bam)
• generate index for BAM files
• OPTIONAL: convevrt BAM to bigWig for visualization
• count overlapping alignments (count matrix)
• standardize count matrix
• run statistical model for analyzing counts
• produce heat map from standardized counts