The mapped transcripts were used in place of the reference annotation.
The consensus map constructed in the previous step was used in place of the reference for seven more iterations of alignment and assembly, after which it was aligned to the reference sequence using SOMA.
The assembled contigs from all of the clusters were used in place of the reference in the second iteration, and the Rmaps were again aligned and assembled to produce a new set of Rmap contigs.
Such signal would preserve the high frequency component common for all tumor samples in a given batch and therefore if used as a denominator in computing the (log2) ratio in place of the standard reference would decrease the noise this high frequency component is responsible for.
The silybin A/B mixture is a suitable alternative to be used in place of the individual reference standards silybin A and B. The method accuracy was evaluated using a negative control spike recovery test at three concentration levels for all six flavonolignans.
As a first step, the optimal model of evolution for all 52 genes was (re determined using an AIC in ModelTEST v3.6 [ 119] in combination with PAUP*, with the appropriately pruned supertree topology being used as the reference tree in place of the default NJ tree.
On their way past the shoe-rental counter, they saw the birthday cake, a four-foot-square confectionery Monopoly board that featured, in place of the usual Atlantic City street names, references to various highlights of Sammeth's life and career.
That is, in the regions where reads mapped, the resulting consensus sequence was inserted in place of the corresponding region in the Los Alamos reference genome.
But Hollywood — a city in which Ames, like his main character, is not entirely at home — invariably darkens things, and in place of the subcultural specificity he mined from Brooklyn and lower Manhattan, you get jokes about valet parking and the porn industry, and in place of Paul Auster and Gore Vidal you get references to Daniel Craig and Jeffrey Katzenberg.
With the magnet in place, scans of the reference material over the desired temperature range, using multiple references, which can be loaded simultaneously if they do not react or melt together, generate a very high accuracy temperature correction curve [11].
