TSSAR specifications

Information


Unique identifier OMICS_03523
Name TSSAR
Interface Web user interface
Restrictions to use None
Programming languages Java, Perl, R
License Apache License version 2.0, GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Fabian Amman <>

Additional information


http://nibiru.tbi.univie.ac.at/TSSAR/workflow

Publication for TSSAR

TSSAR in publications

 (7)
PMCID: 5607370
PMID: 28585937
DOI: 10.1038/ismej.2017.88

[…] aligner (, ). resulting sam files containing mapped reads were converted into sorted and indexed bam files using samtools (). a single alignment run of transcription start site annotation regime (tssar) software was performed to determine start site differences between the transcriptional start site-enriched samples and non-enriched samples in the n-replete and n-depleted samples (). […]

PMCID: 5015018
PMID: 27605472
DOI: 10.1038/srep31597

[…] instructions to remove residual dna contamination., rna-seq was carried out by vertis biotechnologie. data analysis was carried out using the tuxedo protocol for analysis of gene expression and tssar webservice for drna transcription start site analysis. in addition a manual visual processing approach was carried out for each., l luria-bertani medium (10 × 500 ml) was inoculated […]

PMCID: 5167064
PMID: 27540267
DOI: 10.1093/bioinformatics/btw541

[…] to exclude reads mapping to more than a single position from downstream analyses () and many read mapping analysis tools do not address multiple mapped reads (e.g. tsspredator (), tsser () and tssar () for tss detection or varscan 2 [() for single nucleotide polymorphism (snp) detection]. for the latter tools, we assume that they incorporate all reads present in the data set provided […]

PMCID: 4603805
PMID: 26462475
DOI: 10.1186/s12864-015-1993-3

[…] reads just considering the first base of each read., mapping output from drna-seq was split by replicon and coverted to sam format (using samtools 1.2). those sam files were used as input for tssar, a tool for automated de novo tss annotation [], to map all loci with coverage maxima which are enriched in the tex-treated library. default parameters (p-value threshold 0.001, noise threshold […]

PMCID: 4376681
PMID: 25816203
DOI: 10.1371/journal.pgen.1005087

[…] to detect genomic positions, where the difference of observed read starts significantly exceeds the difference of expected read starts. these positions are then defined as tss. we further applied tssar [], an implementation of the drna-seq tss detection method, on our rna-seq data. different to the standard drna-seq experimental setup, the background distribution of read starts was obtained […]


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TSSAR institution(s)
Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria; Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria; Center for RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, NM, USA; Research group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
TSSAR funding source(s)
Supported by the Austrian Science Fund (FWF) projects “In silico annotation of noncoding RNAs and their targets” (AF 0430511), “RNA regulation of the transcriptome” (F43), the German ministry of science (0316165C as part of the e:Bio initiative), and the Deutsche Forschungsgemeinschaft (STA 850/10–2 within the SPP 1258 “Sensory and regulatory RNAs in Prokaryotes”).

TSSAR review

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Amr Galal

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Web
The tools is great, powerful and better than others for detect TSS
just the web tool doesn't give same results as the stand alone one using same parameters