evolution, organisms, changed, drastically, going, single, celled, complex, life, forms, encounter, unfortunately, notion, genetics, modern, established, mid, century, essentially, successful, products, generations, really, nor, study, function, recently, revolution, computers, building, living, discovery, following, observed, various, annotated, genetical, structure, managed, connect, diseases, regions, create, reference, genomes, expect, used, comparing, individuals, specic, traits, nd, deviations, interest, however, information, encoded, cells, hidden, observations, code, epigenetic, factors, whom, known, methylation, currently, adequate, tools, extensions, nding, usually, considered, per, basis, giving, aggregated, value, status, approach, extracting, involves, mapping, identify, sites, compared, identifying, adjacent, method, focuses, possibilities, example, inuence, aim, thesis, provide, insight, analysis, pairwise, extract, mapped, tting, goal, useful, further, manual, conduct, experiments, interpret, results, analaysis, deoxyribonucleic, acid, molecule, encode, instructions, development, due, being, storage, stable, fairly, state, throughout, lifespan, contained, double, helix, meaning, nucleobase, exists, complement, base, themselves, adenine, guanine, thymine, cytosine, complementary, strand, wrapped, preserve, bases, phosphate, nucleobases, establish, moving, denition, sequence, string, length, composed, character, representations, nucleotides, thus, set, alphabet, elements, supposed, represent, general, required, randomness, completely, random, across, species, denoted, restricted, methylcytosine, common, occasionally, deaminates, ammonia, mutation, sense, deamination, process, adding, methyl, substance, substitution, reaction, causes, occur, addition, transformation, according, current, knowledge, type, mammalian, greater, property, havent, explored, furthermore, mostly, cpg, cytosinephosphate, discovered, treating, bisulte, amino, removed, methylated, enables, technique, actually, called, sequencing, formats, specications, text, based, le, representing, peptide, represented, abbreviation, corresponding, contains, headers, describe, symbol, total, mandatory, optional, parameter, separated, rst, whitespace, description, concerned, focus, using, nucleotides[], possible, content, encoding, combination, omitted, uncommon, ve, presented, recommended, less, consistent, human, gene, bone, gla, protein, additional, quality, scores, computed, formula, log, qis, pis, error, probability, prediction, correct, imply, million, outline, consists, followed, option, itself, similar, finally, ascending, smallest, highest, [\]^_, abcdefghijklmnopqrstuvwxyz, lling, overall, lower, original, split, multiple, strongly, discouraged, splitting, markers, overlap, parsing, generally, storing, smaller, filed, data, int, bitwise, ag, leftmost, position, modications, match, elds, hhhhhhhhhhghhghhhhhfhhhhhfffffe, ee[, ]b[d[ed, [[^, alignment, map, delimited, consisting, section, leds, entry, commonly, colon, multitude, below, produced, readable, software, binary, compact, compressed, nature, luckily, conversion, simple, tag, edit, mismatches, bismark, hhh, hhhhx, hx, hh, difference, introduced, later, version, replaced, reect, insertions, deletions, whereas, sensible, dene, essence, task, classication, distributing, mathematical, given, objective, maximize, minimize, accuracy, closer, inspection, dependent, equal, cardinality, classes, metric, illustration, class, classied, incorrectly, situation, predicting, constant, improve, amount, potential, measurements, discuss, outcomes, respect, confusion, matrix, measure, performance, supervised, learning, algorithms, comparisons, actual, examining, objects, compare, positive, false, negative, fortunately, interested, context, trivial, identity, observing, potentially, predict, purpose, strength, hypothesis, question, directly, affect, nother, detect, pinpoint, average, behavior, especially, designed, pariwise, looking, individually, manner, within, discard, informative, chromosomename, chromosome, leftmostloctaion, integer, location, rightmostlocation, rightmost, truepositive, falsepositive, falsenegative, truenegative, output, restricts, input, sorted, analyzed, default, destination, coma, csv, myle, directory, script, program, containing, cg, firstly, existence, checked, examination, dened, secondly, initialize, dereferenced, re, initialized, unique, identication, booleans, non, thirdly, checks, whether, occured, writes, releases, memory, manage, minimal, requirement, traverse, expected, express, populated, print, designated, fashion, traversal, processing, identicators, appended, written, complexity, carried, convince, reader, assert, denote, chrs, csuch, distinction, bounds, separately, balanced, granting, user, guaranteed, logarithmic, traversed, receive, upper, assume, maximal, creads, worst, inserting, distinct, search, operation, modifying, larger, include, post, compute, sorts, computing, trickier, variable, achieve, sorting, identiers, traversing, sufcient, inequality, pointer, moved, equality, exclusive, multiply, max, cinchrom, cannot, reduce, zero, package, requires, java, virtual, usage, rjava, library, computations, choice, availability, chosen, language, host, mainly, dealing, motivation, consistency, existing, located, pipeline, conducting, necessary, concentrate, biologists, produce, clearly, unambiguously, studied, breast, cancer, patients, derived, frequent, association, patterns, having, proceed, gathering, taking, samples, treated, chemical, transforms, unmethylated, uracil, leaves, sequenced, advantage, prone, relies, unmehtylated, counted, reality, fragments, provided, control, stored, databases, accessible, bioinformaticians, enthusiasts, trimming, trim, galore, automated, assertion, raw, trimmed, performed, visual, understanding, displays, variations, assist, extra, transformed, cope, converted, sequencer, preprocessing, merged, executed, bowtie, aligner, tted, unreasonable, allow, nessecary, systematic, annomalies, ignore, discrepency, workow, obtaining, command, compliment, dataset, database, download, wget, ftp, trace, ncbi, nlm, nih, gov, sra, srainstant, bystudy, downloaded, unpack, toolkit, fastq, dump, specically, maximum, specify, append, manually, automatically, shown, image, removing, areas, consider, percentage, screenshot, fastqc, bismark_genome_preparation, path_to_bowtie, shared_group, verbose, preparation, stranded, specy, corresponds, mismatched, allowed, legal, preparing, import, described, producepairwisemethylation, yields, discussed, correlation, coefcient, matthews, statistical, initial, previous, assessing, suffer, paradox, varying, inherently, biased, range, extremal, disequilibrium, explore, detail, linkage, loci, developed, similarity, calculated, frequencies, occurrences, dividing, allele, convert, xis, event, subscript, absence, follwing, rid, normalize, theoretical, min, equilibrium, independent, complete, dependence, aggregate, aggregations, behaviour, wider, scale, summing, running, test, normalized, dont, exhibit, biases, caused, proportions, chapter, discusses, future, contributed, topic, orgainsms, relatively, unknown, article, islands, motivator, exploring, poses, tend, namely, transitions, proles, associate, amongst, interesting, laws, classiers, prior, lack, author, purely, hypothetical, unexplored, practical, application, producing, introduction, analyzing, rstly, introcudes, concepts, benecial, obtain, nal, introducing, alternative, preliminaries