ReadXplorer protocols

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description
ReadXplorer computational protocol

ReadXplorer specifications

Information


Unique identifier OMICS_04011
Name ReadXplorer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rolf Hilker <>

Publication for ReadXplorer

ReadXplorer IN pipelines

 (7)
2018
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] of g. oxydans using bowtie2 v2.2.7 [41, 42]. cufflinks and cuffnorm were used to quantify transcript levels [43]., detection of tsss was done with libraries enriched for primary transcripts using readxplorer [44] with the following parameters: (i) only single perfect mappings were considered. (ii) minimum percent of coverage increase was set to 250% and minimum number of read starts to 20. […]

2018
PMCID: 5784534
PMID: 29370758
DOI: 10.1186/s12864-018-4481-8

[…] default parameters. between 96 to 99% of the reads were mapped to the genomic reference (additional file 2: table s2). for visualization and further analysis, the mapped reads were imported into readxplorer [48]., the analysis of the primary 5′-end cdna data with the software readxplorer [48] resulted in the automatic detection of 3987 putative transcription start sites (tss) in the c. […]

2018
PMCID: 5784534
PMID: 29370758
DOI: 10.1186/s12864-018-4481-8

[…] reference (additional file 2: table s2). for visualization and further analysis, the mapped reads were imported into readxplorer [48]., the analysis of the primary 5′-end cdna data with the software readxplorer [48] resulted in the automatic detection of 3987 putative transcription start sites (tss) in the c. diphtheriae nctc 13129 genome. after manual inspection of the automatically detected […]

2017
PMCID: 5423683
PMID: 28486484
DOI: 10.1371/journal.pone.0177278

[…] –ln679996] using tophat2 [16]. two mismatches were allowed to account for possible sequencing errors and allelic variants of the diploid r. solani ag1-ib genome [10]. the rna-seq analysis platform readxplorer [17] was used for the visualization of short read alignments., results of the short read mapping were imported into the platform readxplorer 2.0.1. [17,18]. the r package deseq [19] […]

2017
PMCID: 5423683
PMID: 28486484
DOI: 10.1371/journal.pone.0177278

[…] solani ag1-ib genome [10]. the rna-seq analysis platform readxplorer [17] was used for the visualization of short read alignments., results of the short read mapping were imported into the platform readxplorer 2.0.1. [17,18]. the r package deseq [19] was selected in this work. genes with a minimum fold change of log2 1, and a p-adjusted value smaller than 0.05 were deemed significant., […]

ReadXplorer institution(s)
Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen, Germany

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