Physical Sciences and Mathematics Commons^™

Systematic Evaluation Of The Impact Of Chip-Seq Read Designs On Genome Coverage, Peak Identification, And Allele-Specific Binding Detection, Qi Zhang, Xin Zeng, Sam Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Kele

Department of Statistics: Faculty Publications

Background: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36–50 bps), long (75–100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection.

Results: We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell …

A New Archaeoastronomical Investigation Of The Irish Axial-Stone Circles, Frank T. Prendergast, Clive L. Ruggles

Conference Papers

This paper presents the preliminary results of a project undertaken in 1994 to investigate the astronomical potential of the axial-stone circles (ASCs) of seven or more stones in Counties Cork and Kerry, south-west Ireland. This group of sites is of particular interest in that the monuments in the group bear a striking resemblance to the recumbent stone circles (RSCs) of Aberdeenshire, eastern Scotland, which appear to exhibit a strong pattern of alignment in relation to prominent hilltop summits and the rising and setting position of the moon. The first indications from the Irish data are that similar patterns of alignment …