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HTSstation specifications

Information


Unique identifier OMICS_05369
Name HTSstation
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_05369
Name HTSstation
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for HTSstation

HTSstation citations

 (15)
library_books

The SAGA complex, together with transcription factors and the endocytic protein Rvs167p, coordinates the reprofiling of gene expression in response to changes in sterol composition in Saccharomyces cerevisiae

2017
Mol Biol Cell
PMCID: 5620372
PMID: 28768829
DOI: 10.1091/mbc.E17-03-0169

[…] on the Illumina 2500 HiSeq system according to the manufacturer’s specifications.The mapping of the sequencing data was performed with Bowtie 2.1.0 in end-to-end mode, using the mapping module of the HTSstation analysis platform (). Results can be downloaded (http://htsstation.epfl.ch/mapseq/jobs/e9IBR9xqFdd7scDcgId5/get_results).For each condition (wt, wt-HFI1-TAP, wt-SPT7-TAP, erg3, erg3-HFI1-TA […]

call_split

Large scale genomic reorganization of topological domains at the HoxD locus

2017
Genome Biol
PMCID: 5547506
PMID: 28784160
DOI: 10.1186/s13059-017-1278-z
call_split See protocol

[…] oducts were multiplexed and sequenced with a 100-bp single-end Illumina HiSeq flow cell. Demultiplexing, mapping to the mouse assembly GRCm38 (mm10), and 4C-Seq analysis were performed using the BBCF HTSstation (http://htsstation.epfl.ch and []), according to []. Briefly, the 4C-Seq fragments directly surrounding the viewpoints (2 kb) were excluded for the rest of the analysis. Fragment scores wer […]

library_books

Innate immune sensing of cytosolic chromatin fragments through cGAS promotes senescence

2017
Nat Cell Biol
PMCID: 5826565
PMID: 28759028
DOI: 10.1038/ncb3586

[…] Samples were sequenced by the NextSeq 500 system sequencing with 1x75 cycle (“single read”), “high output” mode (=expected minimal 400mio reads), chemistry “v2”. Sequencing data were processed using HTSstation online software from the Bioinformatics and Biostatistics Core Facility (EPFL, Switzerland). Heat maps were produced from normalized expression data using Cluster 3.0 for computation and JT […]

library_books

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis acting elements

2017
PLoS Genet
PMCID: 5549768
PMID: 28749941
DOI: 10.1371/journal.pgen.1006903

[…] mics Platform of the University of Geneva (Switzerland). Reads were sorted, aligned, translated to restriction fragments and smoothed (11 fragments running mean) using the 4C-seq pipeline of the BBCF HTSstation [] according to ENSEMBL Mouse assembly NCBIM37 (mm9). For the calculation of the 4C-seq signal distribution, reads were normalized to the entire chromosome 10, based on an approach adapted […]

call_split

Transcription facilitated genome wide recruitment of topoisomerase I and DNA gyrase

2017
PLoS Genet
PMCID: 5433769
PMID: 28463980
DOI: 10.1371/journal.pgen.1006754
call_split See protocol

[…] ChIP-Seq analysis was performed using the HTS station pipeline (http://htsstation.epfl.ch/). Single-end sequence reads generated from ChIP-Seq experiments were aligned to the Mtb H37Rv genome (NCBI accession NC_000962.2) using Bowtie [] with default option in HTS station […]

library_books

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

2017
PLoS Biol
PMCID: 5393560
PMID: 28414715
DOI: 10.1371/journal.pbio.2001069

[…] At each time point, DNA sequenced reads were mapped to the mouse genome (Mus musculus NCBIM37 genome assembly [mm9; July 2007]) using bowtie through the HTS station portal (http://htsstation.epfl.ch) []. Duplicate reads were kept to avoid saturation because of high coverage of Hi-seq libraries and DNase I specificities. Quality controls, including the percentage of reads within […]

Citations

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HTSstation institution(s)
School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
HTSstation funding source(s)
Supported by SystemsX.ch, the Swiss Initiative in Systems Biology, through the SyBIT, CycliX, LipidX (FPAD) and DynamiX projects, by the ERC grant SystemsHox.ch, by a Swiss National Science Foundation Sinergia Grant CRSI33_130662 and by the EPFL.

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