During the initial data processing phase of our analysis, we made several interesting discoveries.
To improve the quality of initial data processing, the results of different scanning methods can be combined from homology search of a nucleotide consensus sequence, homology search of deduced protein sequences and involvement of reference databases of known organisms [ 14- 17].
for initial data processing (before computation of averages).
Rather than gathering identifiable PHI information into a central repository for analysis, a distributed system moves some of the initial data processing, such as counting aggregated episodes of care (see below), to the site where the data is being collected.
Initial data processing and base calling of 100 base pair (bp) reads was done with RTA 1.17.20 (HiSeq Control Software 2.0.5, Illumina, San Diego, CA, USA) and sequence quality filtering script was executed in the Illumina CASAVA software (V1.8.2, Illumina, San Diego, CA, USA) by Ambry Genetics (Aliso Viejo, CA, USA).
The GenomeStudio Methylation Module Package (version 1.9, Illumina) was used for initial data processing, allowing for the calculation of methylation values (expressed as β-values, ranging from 0 to 1) and detection P-values for 482,421 individual probes spanning the 22 autosomes and sex chromosomes.
Initial data processing and base calling, including extraction of cluster intensities, was done using RTA 1.12.4 (HiSeq Control Software 1.4.5 Illuminaa).
O.R.H. helped to secure the VLT time, prepared the VLT phase II programme, performed the initial data processing, and developed the rotational light-curve colour solight-curve colourent of solutiond its implicandons.
Initial data processing and analyses were performed by K.C., R.K., D.R.K. and M.J.Z. with the guidance of A.M. and J.L.R. H.G. and E.K.S. generated WGBS libraries under the guidance of A.G. R.P. assisted with flow cytometry analysis.
