424 research outputs found
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Assessment of transcript reconstruction methods for RNA-seq
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.This work was supported by European Molecular Biology Laboratory, US National Institutes of Health/NHGRI grants U54HG004555 and U54HG004557, Wellcome Trust grant WT098051, and grants BIO2011-26205 and CSD2007-00050 from the Ministerio de Educación y Ciencia
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Systematic evaluation of spliced alignment programs for RNA-seq data
High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions
Dependence of atmospheric muon flux on seawater depth measured with the first KM3NeT detection units
Tensor Analyzing Powers for Quasi-Elastic Electron Scattering from Deuterium
We report on a first measurement of tensor analyzing powers in quasi-elastic
electron-deuteron scattering at an average three-momentum transfer of 1.7
fm. Data sensitive to the spin-dependent nucleon density in the deuteron
were obtained for missing momenta up to 150 MeV/ with a tensor polarized
H target internal to an electron storage ring. The data are well described
by a calculation that includes the effects of final-state interaction,
meson-exchange and isobar currents, and leading-order relativistic
contributions.Comment: 4 pages, 3 figure
The Antares Collaboration : Contributions to the 34th International Cosmic Ray Conference (ICRC 2015, The Hague)
The ANTARES detector, completed in 2008, is the largest neutrino telescope in the Northern hemisphere. Located at a depth of 2.5 km in the Mediterranean Sea, 40 km off the Toulon shore, its main goal is the search for astrophysical high energy neutrinos. In this paper we collect the 21 contributions of the ANTARES collaboration to the 34th International Cosmic Ray Conference (ICRC 2015). The scientific output is very rich and the contributions included in these proceedings cover the main physics results, ranging from steady point sources, diffuse searches, multi-messenger analyses to exotic physics
Search for muon-neutrino emission from GeV and TeV gamma-ray flaring blazars using five years of data of the ANTARES telescope
The ANTARES telescope is well-suited for detecting astrophysical transient
neutrino sources as it can observe a full hemisphere of the sky at all times
with a high duty cycle. The background due to atmospheric particles can be
drastically reduced, and the point-source sensitivity improved, by selecting a
narrow time window around possible neutrino production periods. Blazars, being
radio-loud active galactic nuclei with their jets pointing almost directly
towards the observer, are particularly attractive potential neutrino point
sources, since they are among the most likely sources of the very high-energy
cosmic rays. Neutrinos and gamma rays may be produced in hadronic interactions
with the surrounding medium. Moreover, blazars generally show high time
variability in their light curves at different wavelengths and on various time
scales. This paper presents a time-dependent analysis applied to a selection of
flaring gamma-ray blazars observed by the FERMI/LAT experiment and by TeV
Cherenkov telescopes using five years of ANTARES data taken from 2008 to 2012.
The results are compatible with fluctuations of the background. Upper limits on
the neutrino fluence have been produced and compared to the measured gamma-ray
spectral energy distribution.Comment: 27 pages, 16 figure
Transverse-target-spin asymmetry in exclusive -meson electroproduction
Hard exclusive electroproduction of mesons is studied with the
HERMES spectrometer at the DESY laboratory by scattering 27.6 GeV positron and
electron beams off a transversely polarized hydrogen target. The amplitudes of
five azimuthal modulations of the single-spin asymmetry of the cross section
with respect to the transverse proton polarization are measured. They are
determined in the entire kinematic region as well as for two bins in photon
virtuality and momentum transfer to the nucleon. Also, a separation of
asymmetry amplitudes into longitudinal and transverse components is done. These
results are compared to a phenomenological model that includes the pion pole
contribution. Within this model, the data favor a positive
transition form factor.Comment: DESY Report 15-14
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