[Verse 1] Cytosine wearing a shadow, methyl tag on its back, CpG islands cluster where the shores start to crack, Bisulfite melts the code, unmethylated bases turn, Bismark reads the ashes, MethylDackel counts what burns, EPIC array checks the same spot a million times over, Long reads with modkit call it straight, no chemical cover, DSS and methylKit trace the drift zone, the DMR, Epigenetic clock ticking — tells your cells how old they are. [Chorus] CpG, TSS, follow the trail, Methyl mark the silence, open chromatin exhale, Peaks and loops and motifs, structure hides in the strand, Read the shadow on the genome, computational hand. [Verse 2] Tn5 cuts where the nucleosome ain't holding tight, ATAC-seq maps the open rooms, DNase does the same fight, Fragment size periodicity — a hundred-and-forty-seven hum, Mitochondrial reads get filtered, only nuclear signal come, FRiP tells you the fraction landed where it should, TSS enrichment spikes up if your prep's actually good. [Verse 3] ChIP-seq drags the antibody, CUT&RUN cuts closer in, CUT&Tag tags it directly, thinner background, thinner skin, MACS3 calls the summits, IDR checks if they're true twice, Blacklist regions flagged — mapping artifacts, not nice, PWM built from aligned sites, information content tall, Logo towers where it's certain, flat where letters could fall, MEME and HOMER discover, FIMO scans the line, JASPAR keeps the library — motif matched, promoter fine. [Verse 4] Hi-C crumples the chromosome, Micro-C zooms in tighter, Contact matrix counts collisions, ICE makes the bias lighter, Eigenvector splits the genome, A compartment, B compartment too, TADs are neighborhoods, loops are handshakes holding through, Cooler stores it, cooltools reads it, Juicer squeezes the file down, Structure folded in the nucleus, invisible in town. [Bridge] Single cell ATAC, one nucleus, one accessible map, Single cell DNA-seq counts the copy number gap, Basenji, Enformer, transformers reading far, Attribution maps the pixel, TF-MoDISco finds the scar, In-silico mutagenesis — flip a base, watch it react, The model dreams in adenine and calls it fact. [Verse 5] VCF holds the variants, GATK calls them clean, Phasing haplotypes together, linkage disequilibrium seen, GWAS scans a million snips, Manhattan plots peak high, Fine-mapping narrows credible sets, causal signal don't lie, eQTLs link the variant to the gene it moves, Colocalization checks the peaks, causal path it proves. [Chorus] CpG, TSS, follow the trail, Methyl mark the silence, open chromatin exhale, Peaks and loops and motifs, structure hides in the strand, Read the shadow on the genome, computational hand. [Outro] Methyl, motif, matrix, fold — the strand keeps a story that computation told.
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