It has problems on deletion and reaction bias of RNA ligase.
Additionally, as the sampling from high-throughput sequencers is not always random across the genome, the problem of inferring deletions is conflated with the problem of detecting sampling bias, particularly for hemizygous deletions.
The problem of parallel deletions and insertions can be overcome using maximum likelihood methods by making use of transition probabilities [ 12].
Each vertex in G may be a member of many different dense subgraphs and thus we formulate the problem of identifying deletions as follows: For each connected component d∈ G and for each set of vertices that form a maximal clique C in d, report C as deleted if | C|≥ k where k is some threshold of evidence.
However, in vivo studies of microRNA function by removal of Dicer share a common problem that deletion of Dicer does not immediately result in microRNA loss of function.
In P. ananatis, the discovery of ccdA, the only major CD encoded by this bacterium, almost fully addressed the problem because deletion of this gene virtually eliminated the cellular degradation of cysteine, thereby drastically increasing its synthesis (Takumi et al. 2017).
While large genomic deletions have already been found and replicated, the problem of identifying small deletions remains an unmet challenge.
The problem of the phoneme deletions still remains, because there are always graphemes that do not originate any phoneme.
In particular, the problem of track extraction and deletion is apparently not yet satisfactorily solved within this framework.
We propose the integrated Structural Variant calling Pipeline (iSVP), which combines existing SV detection methods and resolves this problem by selecting a reliable subset of deletion calls and unifying duplicated entries.
Most recent work on error correction has concentrated on correcting Illumina reads where substitutions is the dominant error type, and so the more challenging problem of correcting insertions and deletions is addressed only by a few works (Salmela, 2010; Salmela and Schröder, 2011).
