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