The GMAP alignment method, with stringent match criteria (using only high-quality reads, unique mappings, multiple-reads SNP support; details in Materials and Methods), produced a total of 10,778 predicted SNPs.
Thus, using standard methods with less stringent filters leads to the prediction of thousands of small ORFs, most of which are not likely to be translated [ 14].
The method was developed with stringent computational and data storage efficiency requirements in mind and is demonstrated by mapping snow depth on the Ethan Allen Firing Range in northern Vermont, USA.
With the decrease in runtime, permutation tests for significance become a feasible option, resulting in increased power compared with stringent methods for multiple hypothesis correction.
First, the study includes a large and representative sample of the general population, with a high response rate, and rigorously standardized methods for data collection with stringent quality control.
Pathway analysis in combination with stringent statistical methods provides a strong indication for the quality of the microarray measurement.
High-resolution mass spectrometry provides very accurate precursor ion masses and combined with stringent statistical methods enhances the certainty of peptide identification [ 26].
For instance, the GMAP alignment method and the Maq analysis method have been applied in soybean with stringent matching criteria (using only high-quality reads, unique mappings, multiple-reads SNP support) for high-throughput SNP discovery through RRL resequencing.
Urinary samples were then stored at −20°C in the study centers and subsequently sent to the core lab at the Centre Hospitalier Universitaire Vaudois (CHUV, Lausanne, Switzerland) for centralized analyses with standard methods and stringent internal quality controls.
As an example, RAP1 was assigned to a set of 126 regulated genes using our method, while only 70 targets were identified with stringent P-value cutoff.
