Skunk River Review Fall 1995, Vol 7

https://openspace.dmacc.edu/skunkriver/1016/thumbnail.jp

Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads

Since the emergence of next-generation sequencing (NGS) technologies, great effort has been put into the development of tools for analysis of the short reads. In parallel, knowledge is increasing regarding biases inherent in these technologies. Here we discuss four different biases we encountered while analyzing various Illumina datasets. These biases are due to both biological and statistical effects that in particular affect comparisons between different genomic regions. Specifically, we encountered biases pertaining to the distributions of nucleotides across sequencing cycles, to mappability, to contamination of pre-mRNA with mRNA, and to non-uniform hydrolysis of RNA. Most of these biases are not specific to one analyzed dataset, but are present across a variety of datasets and within a variety of genomic contexts. Importantly, some of these biases correlated in a highly significant manner with biological features, including transcript length, gene expression levels, conservation levels, and exon-intron architecture, misleadingly increasing the credibility of results due to them. We also demonstrate the relevance of these biases in the context of analyzing an NGS dataset mapping transcriptionally engaged RNA polymerase II (RNAPII) in the context of exon-intron architecture, and show that elimination of these biases is crucial for avoiding erroneous interpretation of the data. Collectively, our results highlight several important pitfalls, challenges and approaches in the analysis of NGS reads

Advances in Auctions

As a selling mechanism, auctions have acquired a central position in the free market economy all over the globe. This development has deepened, broadened, and expanded the theory of auctions in new directions. This chapter is intended as a selective update of some of the developments and applications of auction theory in the two decades since Wilson (1992) wrote the previous Handbook chapter on this topic

Debris cloud expansion around a residual rod behind a perforated plate target

The debris cloud expansion around a residual rod behind a perforated plate target has been studied by means of the laser stroboscope and the flash X-ray observation technique. Especially the bulging at the target rear side, the breaking of the bulge, its fragmentation and the cloud expansion nearby and far from the target are investigated. Rods of tungsten sinter alloy, steel and Ti with aspect ratios 6 to 15 are launched against steel and Al targets at 1250 and 1700 m/s in full and half scales. The cloud expansion scales and depends only weakly on the parameters varied here. The shape of the cloud behaves roughly elliptically. For rod and target material densities pp bigger than pT, the rod fragments show a smaller lateral spread than the target fragments. Target fragments are found within the total cloud volume. Fragments at equal radial distance from the target rear side have roughly the same velocity. The debris also have been caught by a soft catcher for tungsten sinter alloy and steel rods against steel plates in full scale. The evaluation and data reduction deliver information about number, size, shape, material, mass and angle of the fragments. The accumulated number of fragments versus mass can be described by a Mott distribution function. The angular distribution shows a maximum. Increasing impact velocity extends the lateral spread of the particles