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TraV specifications

Information


Unique identifier OMICS_03570
Name TraV
Alternative name Transcriptome Viewer
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Output format TSV,GFF
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Maintained Yes

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Maintainer


  • person_outline Heiko Liesegang <>

Publication for Transcriptome Viewer

TraV in publications

 (4)
PMCID: 5398030
PMID: 28473807
DOI: 10.3389/fmicb.2017.00642

[…] nos operon coding for the nitrous oxide reductase protein complex (ec 1.7.2.4; figure ). the different transcriptional units were deduced from the rna sequencing data (figure ) and visualized using trav (dietrich et al., ). the rna sequencing experiments revealed a 10- to 100-fold increase in transcription for the denitrification genes under anaerobic conditions. involved promoter regions […]

PMCID: 4872519
PMID: 27242752
DOI: 10.3389/fmicb.2016.00737

[…] usa) and shotgun transcriptomic reads were mapped to the reference genome sequence using bowtie 2 (v1.0.0; ). mapping results were used to compare differentially expressed genes. application of the transcriptome viewer (trav) () visualized the data in tables or plots. to compare the rnaseq experiments, the mapped data were normalized and presented as npkm (nucleotide activities per kilobase […]

PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] quantitative trait loci (sqtl) can be obtained using spliceplot []. splice graphs can be produced using spliceseq [], and splicingviewer [] plots splice junctions and alternative splicing events. trav [] is a visualization tool that integrates data analysis, but its analytical methods are not applicable to large genomes., owing to the complexity of transcriptomes, efficient display […]

PMCID: 4374763
PMID: 25811873
DOI: 10.1371/journal.pone.0120759

[…] genome of b. licheniformis dsm13 (accession number ae017333.1) [] using bowtie2 [], allowing 2% aberration. the output sam files were converted to tds-files by the program samtotds and visualized by trav []. the sequencing raw data are available at the nih short read archive (srp035551). to compare phage dna mappings with different read numbers, a coverage analysis was performed using npkm […]

TraV institution(s)
Abteilung für Angewandte und Genomische Mikrobiologie, Institut für Mikrobiologie und Genetik, Norddeutsches Zentrum für Mikrobielle Genomforschung, Georg-August-Universität Göttingen, Göttingen, Germany
TraV funding source(s)
Supported by the Bundesministerium fur Bildung und Forschung (FKZ-0315387).

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