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
More filters
Journal ArticleDOI
Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation
Katia Ancelin,Laurène Syx,Laurène Syx,Laurène Syx,Maud Borensztein,Maud Borensztein,Noémie Ranisavljevic,Noémie Ranisavljevic,Ivaylo Vassilev,Ivaylo Vassilev,Ivaylo Vassilev,Luis Briseño-Roa,Tao Liu,Eric Metzger,Nicolas Servant,Nicolas Servant,Nicolas Servant,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Chong-Jian Chen,Roland Schüle,Edith Heard,Edith Heard +23 more
TL;DR: It is proposed that KDM1A plays critical roles in establishing the correct epigenetic landscape of the zygote upon fertilization, in preserving genome integrity and in initiating new patterns of genome expression that drive early mouse development.
Journal ArticleDOI
Correspondence between Resting-State Activity and Brain Gene Expression.
Guang-Zhong Wang,T. Grant Belgard,Deng Mao,Leslie Chen,Stefano Berto,Todd M. Preuss,Hanzhang Lu,Daniel H. Geschwind,Genevieve Konopka +8 more
TL;DR: This work identifies significant correlations between gene expression in the brain and functional activity by comparing fractional amplitude of low-frequency fluctuations (fALFF) from two independent human fMRI resting-state datasets to regional cortical gene expression from a newly generated RNA-seq dataset and two additional gene expression datasets to obtain robust and reproducible correlations.
Journal ArticleDOI
Pathway analysis of systemic transcriptome responses to injected polystyrene particles in zebrafish larvae
TL;DR: The results show limited spreading of particles within the larvae after injection during the blastula stage, which is in contrast to injection of PS particles in the yolk of 2-day old embryos, which resulted in redistribution of the PS particles throughout the bloodstream, and accumulation in the heart region.
Journal ArticleDOI
ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS-STING.
Konrad Aden,Florian Tran,Go Ito,Go Ito,Raheleh Sheibani-Tezerji,Simone Lipinski,Johannes Kuiper,Markus Tschurtschenthaler,Markus Tschurtschenthaler,Svetlana Saveljeva,Joya Bhattacharyya,Robert Häsler,Kareen Bartsch,Anne Luzius,Marlene Jentzsch,Maren Falk-Paulsen,Stephanie T. Stengel,Lina Welz,Robin Schwarzer,Björn Rabe,Winfried Barchet,Stefan Krautwald,Gunther Hartmann,Manolis Pasparakis,Richard S. Blumberg,Stefan Schreiber,Arthur Kaser,Philip Rosenstiel +27 more
TL;DR: An unexpected role of ATG16L1 is demonstrated in coordinating the outcome of IL-22 signaling in the intestinal epithelium, which potentiates endogenous ileal inflammation and causes widespread necroptotic epithelial cell death in Atg16l1&Dgr;IEC mice.
Journal ArticleDOI
Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Wei-Hung Pan,Felix Sommer,Felix Sommer,Maren Falk-Paulsen,Thomas Ulas,Philipp Best,Antonella Fazio,Priyadarshini Kachroo,Anne Luzius,Marlene Jentzsch,Ateequr Rehman,Fabian Müller,Thomas Lengauer,Thomas Lengauer,Joern Walter,Sven Künzel,John F. Baines,John F. Baines,Stefan Schreiber,Andre Franke,Joachim L. Schultze,Joachim L. Schultze,Fredrik Bäckhed,Fredrik Bäckhed,Philip Rosenstiel +24 more
TL;DR: This study represents the first genome-wide analysis of microbiota-mediated effects on maturation of DNA methylation signatures and the transcriptional program of IECs after birth and indicates that the gut microbiota dynamically modulates large portions of the epithelial transcriptome during postnatal development, but targets only a subset of microbially responsive genes through theirDNA methylation status.
References
More filters
Journal ArticleDOI
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Trimmomatic: a flexible trimmer for Illumina sequence data
TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.