Because the length of discernible haplotype regions is usually limited by read length, we focus on gene-sized alignments as would be found in transcriptome studies.
However, our statistical power to detect allelic imbalance is limited by read depth and, therefore, this estimate of 4.6% is a lower bound.
Since the detection of insertions is limited by read length, we define and identify large insertions of various sizes by examining the nature of unaligned segments between HSPs generated using cross_match.
We will discuss how each method can be used to characterise genomic rearrangements, with the exception of local assembly approaches that are still limited by read length and cost (Alkan et al., 2011b).
Even though a deletion of an arbitrary size can be detected as long as it is covered by one or more reads, the size of insertions that can be directly detected in full is limited by the read length.
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Earlier Lygus transcriptome assemblies were limited by low read depth, or because they focused on specific conditions.
The longest M region (28,934 nt) corresponds to a region containing a Ty (yeast retrotransposon) and the rDNA clusters (only one cluster is annotated in the reference genome) on chromosome XII, whereas many M regions exhibit much shorter lengths with a minimal length of 50 nt, limited by the read length resolution.
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Because of this effect, the block size of the 3D memory architecture is limited by suitable reading operation.
