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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Lamins Organize the Global Three-Dimensional Genome from the Nuclear Periphery
Xiaobin Zheng,Jiabiao Hu,Sibiao Yue,Lidya Kristiani,Miri Kim,Michael E.G. Sauria,James Taylor,Youngjo Kim,Yixian Zheng +8 more
TL;DR: It is revealed that lamin loss causes expansion or detachment of specific LADs in mouse ESCs, and a significant correlation between transcription changes and the interaction changes of active and inactive chromatin domains is found.
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Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
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TL;DR: The comprehensive transcriptome at single-cell resolution profiled in this study paves the way for future mechanistic studies of the gene-regulatory networks governing mammalian organogenesis.
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The transcription factor XBP1 is selectively required for eosinophil differentiation
Sarah E. Bettigole,Raphael Lis,Stanley Adoro,Ann-Hwee Lee,Lisa A. Spencer,Peter F. Weller,Laurie H. Glimcher +6 more
TL;DR: Evidence that granulocyte subsets can be distinguished by their differential reliance on secretory-pathway homeostasis is presented, showing an unexpectedly selective and absolute requirement for XBP1 in eosinophil differentiation without an effect on the survival of basophils or neutrophils.
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Cell–matrix signals specify bone endothelial cells during developmental osteogenesis
Urs H. Langen,Mara E. Pitulescu,Jung Mo Kim,Rocio Enriquez-Gasca,Kishor K. Sivaraj,Anjali P. Kusumbe,Amit Singh,Amit Singh,Jacopo Di Russo,M. Gabriele Bixel,Bin Zhou,Lydia Sorokin,Juan M. Vaquerizas,Ralf H. Adams +13 more
TL;DR: It is reported that embryonic and early postnatal long bone contains a specialized endothelial cell subtype, termed type E, which strongly supports osteoblast lineage cells and later gives rise to other endothelium cell subpopulations.
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Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury
Peter Arthur-Farraj,Peter Arthur-Farraj,Peter Arthur-Farraj,Claire Morgan,Martyna Adamowicz,Jose A. Gomez-Sanchez,Shaline V. Fazal,Anthony Beucher,Bonnie Razzaghi,Rhona Mirsky,Kristjan R. Jessen,Timothy J. Aitman,Timothy J. Aitman +12 more
TL;DR: A combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury shows that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and it is demonstrated that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells.
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.