TSSpredator protocols

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TSSpredator specifications

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Unique identifier OMICS_07345
Name TSSpredator
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.04
Stability Stable
Maintained Yes

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Publication for TSSpredator

TSSpredator in pipeline

2017
PMCID: 5312081
PMID: 28196958
DOI: 10.1128/mBio.02041-16

[…] per nucleotide were calculated and normalized to the total number of reads. the resulting wiggle files were visualized with the integrated genome browser, version 6.5.3 (). tsss were predicted with tsspredator version 1.05 (). the numbers of reads mapped to a gene in the sense and antisense directions were calculated. degs (exhibiting at least 2-fold changes in expression) were screened via […]

TSSpredator in publications

 (8)
PMCID: 5467207
PMID: 28585540
DOI: 10.1038/ncomms15774

[…] normalized to the number of reads in each library, and then multiplied by the median number of reads across all libraries to restore the data range. transcription start sites were identified using tsspredator using 90th percentile normalization., rna-seq data that support this study have been deposited in ncbi geo, which are accessible with the accession number gse80786. the following ncbi […]

PMCID: 5449619
PMID: 28334889
DOI: 10.1093/nar/gkx168

[…] in . for a detailed description of the drna-seq and hfq rip-seq read mappings and their normalization see ., transcription start sites were predicted based on the normalized wiggle files using tsspredator (http://it.inf.uni-tuebingen.de/tsspredator) () applying the ‘more strict’ parameter presets. to detect potential promoter motifs, sequence regions corresponding to 50 nt upstream […]

PMCID: 5312081
PMID: 28196958
DOI: 10.1128/mBio.02041-16

[…] there are 34 predicted early promoters on the basis of the occurrence of an overrepresented consensus motif (), to retrieve additional early transcripts, the threshold for “enrichment factor” of the tsspredator program used to predict 5′ ends from drna-seq data was decreased to 0.1 from the 2.0 default setting. in this way, 21 additional 5′ ends associated with the early consensus motif whose […]

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

[…] it is still common practice 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 […]

PMCID: 4983044
PMID: 27519343
DOI: 10.1186/s12864-016-2920-y

[…] data range, each graph was then multiplied by the minimum number of mapped reads calculated among all libraries., the tsss were predicted based on the normalized coverage files obtained from tsspredator version 1.06 [] using the “super specific” parameter set but with a minimal enrichment factor of 2.5 instead of 3.0., the read mapping data underlying the detected tsss were visually […]

TSSpredator institution(s)
Research Center for Infectious Diseases (ZINF), University of Würzburg, Würzburg, Germany

TSSpredator review

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Amr Galal

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Desktop
The tool is really awesome with many different options, but depend on ready files and in compare with new tools could be less than them