The proposed framework contains the classical credibility theory as a special case and is based on the idea of varying the trimming threshold level to investigate the sensitivity of the credibility premium.
Reads were aligned to the S288c reference genome R64-1-1 R64-1-1 R64-1-1.8) (Li and Dusing 2009), allowing six mismatches and using quality trimming (threshold of Phred = 20).
PEAR was used with default parameter settings with the exception of the Phred scale quality score trimming threshold, which was set to 20.
The tool also incorporates novelties for the filtering of windows in RC profiles - thus reducing the amount of false positives, including a PEM-based filter, a method that automatically sets trimming thresholds and a sensible window filter that replaces the removal of low quality reads.
To eliminate low quality nucleotides, raw Illumina reads were trimmed using a custom Perl script with windowed adaptive trimming (Phred quality threshold of 20 and minimum read length of 20 nt).
Reads and read stretches of poor quality bases were removed and trimmed with filter threshold at quality score (Q ≥0.05), ambiguous nucleotide (N ≤2), and length trimming (N ≥30) before de novo transcriptome assembly.
The resulting reads were mapped to the baboon genome (Panu2.0) using the efficient short-read aligner bwa 0.5.9 (Li and Durbin, 2009), with a seed length of 25 bases, a maximum edit distance of two mismatches in the seed, a read trimming quality score threshold of 20, and the default maximum edit distance (4% after trimming).
Every pixel comprises a preamplifier, shaper, discriminator (with a 6 bit DAC for threshold trimming), a configurable 4/8/12 bit counter with double buffering, as well as readout, control and test circuitry.
During the assembly phase, prior to the physical mounting of the plaquettes on the disks a thorough electronic test is necessary to check each channel for functionality, noise level, required threshold trimming and bump-bond quality.
