CopywriteR: DNA copy number detection from off-target sequence data.

Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.

A Forgotten Original or an Original Copy? On MS. Douce 387 in the Bodleian Library: Collecting Early Modern Festival Books

Focusing on one manuscript, today in the Bodleian Library, Oxford, this chapter deals with the question how early modern objects became collectable items. The manuscript is categorized as MS. Douce 387 and its name indicates that it came from the collection of Francis Douce (1757–1834), who was keeper of manuscripts in the British Museum from 1799 until 1811. MS. Douce 387 is described in the catalogue of the Douce’ian collection as the “presentation copy with coloured designs by Marten de Vos and others” of the 1595 printed festival book Descriptio publicae gratulationis … in adventu … Ernesti archiducis Austriae. This festival book, printed in Antwerp’s Plantin-Moretus press, was commissioned by the magistrate of the city of Antwerp to commemorate the Joyous Entry of Archduke Ernest of Austria from June 1594; that an “archducal copy” bound in red velvet was commissioned as well and was owned by the Archduke is know as well. However, first research showed that Oxford copy cannot be this “archducal copy” or Marten de Vos’s artist’s copy even though it is the only know version with a handwritten text and hand-drawn illustrations. It rather should be examined as something totally different altogether. The main question remains why someone then commissioned a hand made version of this festival book, something unknown for other books of this genre? Why would someone between 1600 and 1800 sit down and copy texts and prints from a collectable book? Why was there such an on-going interest in early modern festival books? Could this manuscript be the only later made copy of the “archducal volume” or is it rather a forgery made for the European collectors’ market?