Exact(3)
One can simulate infinite dimensionality by choosing for each of the mixtures a different random set of 30 normalized vectors from the cube (again maintaining the specified overlap among mixture pairs).
Of the 7,174 transcription start sites that satisfied the specified overlap threshold, ∼83% differed by ≤100 nt (Fig. 9A).
Of the 7,174 transcription termination sites that satisfied the specified overlap threshold, ∼69% differed by ≤100 nt (Fig. 9B).
Similar(57)
For the assembly, we used a specify overlap percent identity cutoff (p) of 93.
The CAP3 -p option specifies overlap percent identity cutoff, while the -h option specifies the maximum alignment overhang percentage.
The CAP3 -p option specifies overlap per cent identity cut-off, while the -h option specifies the maximum alignment overhang percentage.
The reads within individual clusters were assembled into contigs using tgicl run with the -O '-p 80 -o 40' parameters, specifying overlap percent identity and length cutoff for cap3 assembler.
The reads within individual clusters were assembled into contigs using TGICL run with the -O '-p 80 -o 40' parameters, specifying overlap percent identity and minimal length cutoff for cap3 assembler.
However, all of those cases corresponded to positions where adjacent reads overlapped by only ~25nt, the specified minimum overlap allowed between two sequences for collapse into a contig for our assembly (see Materials and Methods; Figure 4B, positions ~23k, ~54k, ~88k, ~91k, ~94k).
These notions are often vaguely specified and overlapping in their definitions.
The transcription factor ChIP seq data are summarized by scores, ranging from 6 to 1000, measuring strength of evidence for binding within specified, sometimes overlapping, chromosomal bins ('clusters'clusters
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