A combination of picard tools (1.107), GATK (2.8.1) and FastQC (0.10.1) were used to generate quality control metrics.
The 'References' section states that this process requires a reference genome, a file containing regions to be filtered out for certain analysis steps and a file containing genomic regions relevant for the purpose of generating quality control statistics and plots.
In addition, a single lot of pooled convalescent serum from PEDV infected pigs was used to generate quality control standards that gave high and low optical density (high OD = 2.0 to 2.5; low OD = 0.5 to 1.0; and negative OD < 0.2).
In general, the processes for generating quality controlled and functional reconstructions of metabolism are well established and available elsewhere [ 15, 16].
Adenoviral vectors were generated, quality controlled, and used as described previously (Kolb et al., 2001; Ferrari et al., 2004; Battista et al., 2006).
The mean (standard deviation (SD)) radiochemical yield generated for quality control was 1,286 (572) MBq, with the high variability due to sensitivity of most of the reagents used and the complexity of the synthesis.
As has been suggested [ 3] a reference set of transcripts should be generated for quality control.
Aggregated data is used to generate a quality control report in PDF format and normalized beta and m values are provided as tabular data (Fig. 2, step 1).
For quantified image processing results, there is a need to generate statistical, quality control and bioinformatics information up to the final hit list.
For extremely deep sequencing, ~200 million clean reads for each sample were generated, with quality control (Q ≥ 20) (Additional file 1: Table S7).
