RNASEQR specifications


Unique identifier OMICS_01263
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Leslie Y. Chen <>

Publication for RNASEQR

RNASEQR in publications

PMCID: 4058285
PMID: 24982889
DOI: 10.1155/2014/529271

[…] (sra, http://www.ncbi.nlm.nih.gov/traces/sra/) with the accession number srp032958., raw data were mapped to the mouse reference genome (mm10 downloaded from ucsc) using tophat (version 2.0.3) and rnaseqr (version 1.0.2) software, respectively [, ]. prebuilt genomic indices were created by bowtie and provided to the alignment software for reads mapping. tophat removes a few low-quality score […]

PMCID: 3760913
PMID: 24019895
DOI: 10.1371/journal.pone.0073071

[…] of the transcriptomic origin of each sequencing read (mapping), this has inspired the development of several novel rna–seq mapping tools, e.g. tophat and tophat2 , mapsplice , rum , and rnaseqr . while all of these rely on fast alignment algorithms such as bowtie , they use different strategies to identify reads from exon–exon junctions, a problem unique to rna–seq data. in general, […]

PMCID: 3530550
PMID: 23300661
DOI: 10.1371/journal.pone.0052403

[…] reference becomes impractical. accordingly, a large number of mapping approaches have been developed in recent years to address this problem, including tophat , splicemap , mapsplice , rum , rnaseqr and contextmap . while these approaches differ in their strategies for mapping reads crossing splice junctions or the use of only an alignment to the genome (e.g. tophat, mapsplice […]

PMCID: 3358662
PMID: 22537048
DOI: 10.1186/1471-2105-13-S6-S9

[…] potential splice sites are annotated based on canonical splice signals and reads spanning these splice sites are identified. in contrast, two more recently published methods, rum [] and rnaseqr [], start with read alignments to both the reference transcriptome and genome. novel splice junctions are then identified by aligning unmapped reads to the genome using blat [] […]

PMCID: 3245260
PMID: 22216246
DOI: 10.1371/journal.pone.0029314

[…] sets, i.e. transcripts, with the same entrez gene id were averaged to represent the expression level of the gene., the illumina's sequences were mapped to refseq genes (i.e. entrez gene id ) using rnaseqr, a new short-read rna sequence mapping tool, and expression levels in rpkm (reads per kilo per million) were calculated (leslie chen, personal communication)., in this study, a gene […]

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RNASEQR institution(s)
Institute for Systems Biology, Seattle, WA, USA; Department of Neurosurgery, Chang Gung University College of Medicine and Memorial Hospital, Kwei-Shan, Taoyuan County, Taiwan, China; Department of Computer Science, National Tsing-Hua University, Hsinchu, Taiwan, China; Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan, China; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg

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