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Indeed, the areas more activated for pseudoword reading overlap with those associated with low versus high frequency word processing (Fiez et al. 1999; Fiebach et al. 2002; Ischebeck et al. 2004; Joubert et al. 2004; Peng et al. 2004).
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Many reads overlap lincRNAs that contain rRNA transcripts, such as the 28S rRNA element in lincRNA chr11 84867425-84942100.
Then all the reads were realigned onto contigs again according to the paired-end reads overlap relationship, and all these contigs were joined into 79,825 scaffold sequences.
For each read overlap set Rr we create a multi-alignment of all the reads and screen out any reads that do not pass the error-rate and correlation tests (described below) to produce a filtered read overlap set R'r⊆Rr.
Coverage is overestimated when reads overlap.
One methylated CpG site is located in the region where the reads overlap.
Notably, 8% of the reads overlap with annotated ncRNAs (Table 1 and Figure 1).
The remaining reads overlap regions of at least two different categories.
The authors argue that this poor performance is likely because Newbler v2.3 inexplicably discards portions of read overlap information.
In the overlap graph, each sequence read in ℛ is a vertex and two vertices are joined by an edge if their corresponding reads overlap.
Since BLASR can find alignments where a contig and a read overlap by only around 100 bases, we use these alignments as a filter.
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