Vancouver Short Read Analysis protocols

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Vancouver Short Read Analysis specifications

Information


Unique identifier OMICS_13970
Name Vancouver Short Read Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format GFF3, SAM, SNVmix, VCF
Output data An image for visualize up to four groupings of data (RNA, exon capture, whole genome and controls)
Output format SVG
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Database management system PostgreSQL
License GNU General Public License version 3.0
Computer skills Advanced
Version 4.0.16
Stability Stable
Maintained Yes

Subtools


  • FindPeaks
  • Variations Database

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Versioning


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Maintainer


  • person_outline Anthony Fejes <>

Additional information


An old version of FindPeaks is also available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks

Publications for Vancouver Short Read Analysis

Vancouver Short Read Analysis in pipelines

 (4)
2016
PMCID: 5028410
PMID: 27703927
DOI: 10.3389/fcimb.2016.00097

[…] and all data is shown as a single donor representative of all 3, or as an average of all 3 donor results, as noted., the alignment bam files were used to identify regions of dna enrichment using the findpeaks peak finder/analysis software (v4.0.16; fejes et al., ). the default parameters were used to identify peaks enriched in the chip samples when compared to the input. the peaks […]

2012
PMCID: 3406964
PMID: 22537144
DOI: 10.1186/1471-2164-13-152

[…] tag count plus 3 (the rounded average median tag count within a bin for all chip-seq data), to reduce the effect of low input count in generating extreme ratios. format conversion was done using the vancouver short read analysis package (http://vancouvershortr.sourceforge.net/). the same procedure was done for all chip-seq data sets to obtain a vector of values for each protein or tf. […]

2011
PMCID: 3030562
PMID: 21297973
DOI: 10.1371/journal.pone.0016330

[…] to identify enrichment for curated gene-sets (www.broadinstitute.org/gsea/) and oncomine (www.oncomine.org) to analyse gata2 expression in leukaemia datasets ., chip-seq peaks were identified using findpeaks 3.1 at fdr ≤0.05 and used to define 400 bp-regions centered around the highest point of significant peaks. non-redundant regions were scored by counting all 200 bp-extended reads within […]

2009
PMCID: 2780926
PMID: 20016685
DOI: 10.1371/journal.pbio.1000256

[…] . this gave 18+6.5 million uniquely placed alignments at 23 million unique positions. each read was extended to 200 bases and overlap profiles were calculated to identify regions of enrichment. findpeaks 3.1.92 was used to estimate the false discovery rate (fdr), giving a probability of <0.001 at 15 overlapping fragments. peaks falling within 100 kb of centromeric gaps or overlapping […]


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Vancouver Short Read Analysis in publications

 (51)
PMCID: 5819082
PMID: 29458332
DOI: 10.1186/s12881-018-0533-9

[…] consortium (exac) (http://exac.broadinstitute.org, accessed august 2015) [], genome aggregation database (gnomad) (http://gnomad.broadinstitute.org, accessed october 2017) [], norwegian germline variations database (http://norgene.no/vcf-miner/, accessed october 2017), clinvar (may 2016) [], uniprot knowledgebase (release march 2016) [] and the pfam protein domain database (v29, december […]

PMCID: 5829913
PMID: 29461204
DOI: 10.7554/eLife.35588.033

[…] note, the sacm1l gene used in this study and previous publications () contains a missense mutation y433f relative to the human genome reference sequence. however, the short genetic variations database (dbsnp) shows that this allele (rs1468542) represents approximately 60% of alleles present in the human population sampled to date. this allele can therefore be viewed […]

PMCID: 5654970
PMID: 29066757
DOI: 10.1038/s41598-017-14176-4

[…] of slc1a3 revealed a heterozygous nucleotide change c.1159 a > c (nm_004172). the variant was not detected in 100 control chromosomes nor listed in the databases dbsnp (short nucleotide variations database), exac (exome aggregation consortium) and evs (exome variant server). analysis of the parental dna revealed the variant in the father, while dna from other family members […]

PMCID: 5549744
PMID: 28792508
DOI: 10.1371/journal.pone.0182572

[…] mutationtaster (http://www.mutationtaster.org), sift (http://sift.jcvi.org/) programs were used to predict the effects of each mutation on protein function. the short genetic variations database (dbsnp 142), the nhlbi exome variant server (evs), the 1000 genomes project (tgp), and the exome aggregation consortium (exac) databases were checked for the presence […]

PMCID: 5549384
PMID: 28789634
DOI: 10.1186/s12864-017-4000-3

[…] and online databanks and bioinformatics tools were used. variation viewer [] (release 1.5) was used as a tool for navigating variant data in ncbi’s databases: dbsnp (snp and multiple small-scale variations database, release 149), dbvar (genomic structural variation database, release december 2015) and clinvar (data base for genomic variation and its relationship to human health, release […]


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Vancouver Short Read Analysis institution(s)
Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
Vancouver Short Read Analysis funding source(s)
This project was supported by the Michael Smith Foundation for Health Research and the Genome British Columbia.

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