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chevron_left Read alignment Known transcript quantification Bioinformatics workflows Alternative splicing visualization Read alignment visualization chevron_right
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RSEQtools specifications

Information


Unique identifier OMICS_04794
Name RSEQtools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C
Computer skills Advanced
Version 0.6
Stability Stable
Requirements
GSL, BlatSuite
Maintained Yes

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Maintainers


  • person_outline Mark Gerstein <>
  • person_outline Lukas Habegger <>

Additional information


http://info.gersteinlab.org/RSEQtools

Publication for RSEQtools

RSEQtools in pipelines

 (4)
2014
PMCID: 3960150
PMID: 24647444
DOI: 10.1371/journal.pone.0091940

[…] a read. the gsnap alignments––formatted as sam files––were sorted so that two reads of each pair is in order of chromosomal location. the resulting sam files were converted into mrf format using rseqtools. with the mrf files as input, the fusionseq (version 0.6.1) pipeline was run with default parameters, until the part that calculates confidence estimates for fusion candidates. “abnormal […]

2014
PMCID: 4007560
PMID: 24564186
DOI: 10.1186/1471-2164-15-154

[…] total of 231 unique samples.figure 1, several methods for sequence alignment and gene expression quantification of rna-seq data have been developed (for review see []) including the tuxedo suite [], rseqtools [], and rsem []. these methods each aim to summarize expression levels based on the number of reads that align to each gene, but differ in their treatment of splice junctions and ambiguous […]

2014
PMCID: 4230839
PMID: 25393313
DOI: 10.1371/journal.pgen.1004773

[…] using bowtie to report the single, best alignment (see for parameters). gene expression was measured as rpkm (sum of nucleotides in gene per million mapped nucleotides per gene kb) using rseqtools (), excluding rrna reads from rpkm calculations. differentially expressed genes (, ) were identified by deseq using the statistical thresholds defined in of >4-fold expression […]

2012
PMCID: 3491412
PMID: 23034185
DOI: 10.1186/gb-2012-13-10-r84

[…] 0.9.4) []. reads were mapped simultaneously to the human genome (ncbi version 36/hg18) and a library containing the sequences of all possible exon splice junctions (ensembl 54 exons) created using rseqtools []. reads were mapped using bowtie (version 0.12.7) [] allowing for a maximum of two mismatched bases and reporting the single best alignment for each read. rpkm values were computed […]


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RSEQtools in publications

 (11)
PMCID: 5892924
PMID: 29634760
DOI: 10.1371/journal.pone.0195771

[…] by the original authors using different mathematical methods including robust multi-array average (rma) normalization [], standardization and normalization of microarray data (snomad)(29), the rseqtools framework [] and cubic spline normalization []. all of these methods are independent of specific housekeeping genes., based on publicly available information, some specimens […]

PMCID: 5894337
PMID: 29184206
DOI: 10.1038/s41593-017-0011-2

[…] outfiltermismatchnoverlmax: 0.1, outfiltermultimapnmax: 50, gene expression values (reads per kilobase of exon model per million mapped; rpkm) were computed from the aligned reads using rseqtools. the exon model used was the composite (union of all overlapping exons) of all transcripts for each gene; a description of this composite model is available both in the rseqtools paper […]

PMCID: 5389521
PMID: 27899593
DOI: 10.1093/nar/gkw1156

[…] reads were aligned to the mouse reference genome (version mm9) using bowtie2 (). splice-junction reads were handled by creation of a pseudo-splice genome, similar to the strategy utilized in rseqtools () and aligned using bowtie2 with standard parameters. reads were filtered post-alignment for a mapq score greater than or equal to 30. the number of exon reads for all refseq genes […]

PMCID: 4887520
PMID: 27247029
DOI: 10.3402/jev.v5.31552

[…] were deployed using the genboree framework and include data analysis and data submission pipelines, and exrna metadata tracking tools. data analysis tools such as the excerpt small rna-seq pipeline, rseqtools long rna-seq pipeline, pathway finder and target interaction finder are available in the genboree workbench. the excerpt pipeline generates a variety of sample-level quality control […]

PMCID: 4777652
PMID: 26855148
DOI: 10.1038/nm.4045

[…] . reads (fastq files) were mapped to the human genome reference sequence (hg19/grc37) using star v2.3.0e, and the resulting bam files were subsequently converted into mapped read format (mrf) using rseqtools, a suite of tools for rna-seq data processing and analysis. mrf files include only the primary alignments as determined by star and do not include reads mapped to the mitochondrial […]


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RSEQtools institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
RSEQtools funding source(s)
Supported by National Institutes of Health.

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