HTSeq—a Python framework to work with high-throughput sequencing data
TLDR
This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.Abstract:
Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an opensource software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. Contact: sanders@fs.tum.deread more
Citations
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MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Krishna R. Kalari,Asha Nair,Jaysheel D. Bhavsar,Daniel R. O'Brien,Jaime I. Davila,Matthew A. Bockol,Jinfu J. Nie,Xiaojia Tang,Saurabh Baheti,Jay B. Doughty,Sumit Middha,Hugues Sicotte,E. Aubrey Thompson,Yan W. Asmann,Jean-Pierre A. Kocher +14 more
TL;DR: The developed MAP-RSeq workflow is a comprehensive computational workflow that can be used for obtaining genomic features from transcriptomic sequencing data, for any genome, and has thus far enabled clinicians and researchers to understand the transcriptomic landscape of diseases for better diagnosis and treatment of patients.
Journal ArticleDOI
Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity.
Phi T. Nguyen,Leah C. Dorman,Simon Pan,Ilia D. Vainchtein,Rafael T. Han,Hiromi Nakao-Inoue,Sunrae E. Taloma,Jerika J. Barron,Ari B. Molofsky,Mazen A. Kheirbek,Anna V. Molofsky +10 more
TL;DR: It is found that neuronal IL-33 instructs microglial engulfment of the extracellular matrix (ECM) and that its loss leads to impaired ECM engulfment and a concomitant accumulation of ECM proteins in contact with synapses, which define a cellular mechanism through which microglia regulate experience-dependent synapse remodeling and promote memory consolidation.
Journal ArticleDOI
Resolving early mesoderm diversification through single-cell expression profiling
Antonio Scialdone,Antonio Scialdone,Yosuke Tanaka,Yosuke Tanaka,Wajid Jawaid,Victoria Moignard,Nicola K. Wilson,Iain C. Macaulay,John C. Marioni,John C. Marioni,John C. Marioni,Berthold Göttgens +11 more
TL;DR: The function of Tal1, a key haematopoietic transcription factor, is studied using knockout mice and it is demonstrated, contrary to previous studies performed using retrospective assays, that Tal1 knockout does not immediately bias precursor cells towards a cardiac fate.
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Molecular Classification of Hepatocellular Adenoma Associates With Risk Factors, Bleeding, and Malignant Transformation
Jean-Charles Nault,Jean-Charles Nault,Gabrielle Couchy,Charles Balabaud,Guillaume Morcrette,Stefano Caruso,Jean-Frédéric Blanc,Yannick Bacq,Julien Calderaro,Valérie Paradis,Jeanne Ramos,Jean-Yves Scoazec,Viviane Gnemmi,Nathalie Sturm,Catherine Guettier,Monique Fabre,Eric Savier,Laurence Chiche,Philippe Labrune,Janick Selves,Dominique Wendum,Camilla Pilati,Alexis Laurent,Anne de Muret,Brigitte Le Bail,Sandra Rebouissou,Sandrine Imbeaud,Christophe Laurent,Jean Saric,Nora Frulio,Claire Castain,Fanny Dujardin,Zin Benchellal,Pascal Bourlier,Daniel Azoulay,Alain Luciani,Georges-Philippe Pageaux,Jean-Michel Fabre,Valérie Vilgrain,Jacques Belghiti,Brigitte Bancel,Emmanuel Boleslawski,Christophe Letoublon,Jean-Christophe Vaillant,Sophie Prevot,Denis Castaing,Emmanuel Jacquemin,Jean-Marie Péron,Alberto Quaglia,François Paye,Luigi Terraciano,Vincenzo Mazzaferro,Marie Christine Saint Paul,Benoit Terris,Paulette Bioulac-Sage,Eric Letouzé,Jessica Zucman-Rossi +56 more
TL;DR: Using sequencing and gene expression analyses, a subgroup of HCA is identified by fusion of the INHBE and GLI1 genes and activation of sonic hedgehog pathway associated with malignant transformation and bleeding, respectively.
Journal ArticleDOI
Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation
Ikuo K. Suzuki,Ikuo K. Suzuki,Ikuo K. Suzuki,David Gacquer,Roxane Van Heurck,Devesh Kumar,Devesh Kumar,Devesh Kumar,Marta Wojno,Marta Wojno,Marta Wojno,Angéline Bilheu,Adèle Herpoel,Nelle Lambert,Julian Cheron,Franck Polleux,Vincent Detours,Pierre Vanderhaeghen +17 more
TL;DR: This study uncovers a large repertoire of recently evolved genes active during human corticogenesis and reveals how human-specific NOTCH paralogs may have contributed to the expansion of the human cortex.
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