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We considered a read to be evidence for an exon-exon junction if it had a unique alignment to a target with zero or one mismatch and no indels and if the alignment extended past the midpoint of the target by a certain overhang amount.
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In typical terms, a genome is considered a read-write mechanism akin to lines of code [91].
Note that we only consider a read cycle where s c ≥ 1, s i + s s ≥ 1, hence F ≥ 2.
Consider a read X and the set of reads that overlap a suffix of X, 𝒪.
Consider a read X that overlaps reads Y and Z, which mutually overlap.
Consider a read r sampled from a position i of the genome.
Consider a read, r i, mapped onto g j with z base-pairs of mismatches.
The basic definition is to consider a read as correctly mapped if the original location is retrieved [ 4].
In this paper we consider a reading scenario with an imperfect coherent light source and no initial entanglement involved.
The DPM counts were carried out for 60 min for each sample, considering a reading window comprising all the energies (0 – 2000 keV counting channels).
Alignment parameters required >85% of the each read's length to map to the reference sequence for it to be considered a mapped read.
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