USeq protocols

USeq specifications

Information


Unique identifier OMICS_00499
Name USeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux, Mac OS
Programming languages Java, R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Requirements Q-Value, DESeq2
Maintained Yes

Versioning


Add your version

Maintainers


  • person_outline David Nix <>
  • person_outline Samir Courdy <>
  • person_outline Kenneth Boucher <>

Additional information


http://useq.sourceforge.net/usage.html

Publication for USeq

USeq IN pipelines

 (3)
2017
PMCID: 5691367
PMID: 28981850
DOI: 10.1093/nar/gkx771

[…] script mark duplicates (http://picard.sourceforge.net.). only unique reads mapping to a single location were retained (see supplementary table s2). hira binding sites were determined using the useq package (v8.6.0) (36). for useq the window size was 200 bp, the extension size was 150 bp. to create the enriched regions, the following parameters were used: -i 2,4 -s 13,1. input dna was used […]

2017
PMCID: 5691367
PMID: 28981850
DOI: 10.1093/nar/gkx771

[…] only unique reads mapping to a single location were retained (see supplementary table s2). hira binding sites were determined using the useq package (v8.6.0) (36). for useq the window size was 200 bp, the extension size was 150 bp. to create the enriched regions, the following parameters were used: -i 2,4 -s 13,1. input dna was used as the normalization control. […]

2017
PMCID: 5691367
PMID: 28981850
DOI: 10.1093/nar/gkx771

[…] dataset divided by 1 million. to normalize the window the chip-seq signal of the treatment was divided by the control signal. venn diagrams and associated empirical p-values were generated using the useq (v7.1.2) tool intersectlists (36). the −t value used was 22 008, as the total number of genes of status ‘known’ and biotype ‘coding’ in ensembl genes 73. the number of iterations used was 1000., […]

USeq institution(s)
Huntsman Cancer Institute, Departments of Research Informatics, University of Utah, Salt Lake City, UT, USA; Oncological Sciences, University of Utah, Salt Lake City, UT, USA
USeq funding source(s)
Supported by the Huntsman Cancer Institute and a grant to the institute from the National Institutes of Health (P01CA24014).

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