motifcounter protocols

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motifcounter specifications

Information


Unique identifier OMICS_16966
Name motifcounter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Requirements
methods, testthat, Biostrings, seqLogo, rmarkdown, knitr, R(>=3.0), prettydoc, MotifDb
Maintained Yes

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Maintainer


  • person_outline Wolfgang Kopp <>

Publication for motifcounter

motifcounter in pipeline

2012
PMCID: 3518223
PMID: 23229897
DOI: 10.1083/jcb.201207189

[…] telomeric subset of reads were extracted using a custom script (motif_counter) incorporating functions from samtools () and standard linux pattern-matching programs (http://sourceforge.net/projects/motifcounter/)., the following stealth rnai sirna were designed and synthesized by life technologies: tr4, coup-tf2, and the stealth rnai sirna negative control med gc duplex #2. cells were seeded […]


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motifcounter in publications

 (3)
PMCID: 5860096
PMID: 28961747
DOI: 10.1093/bioinformatics/btx539

[…] and motifs, demonstrating the improvement. the importance of the order-d model is supported in a case study using cpg-island sequences., the method is available as a bioconductor package named ’motifcounter’ https://bioconductor.org/packages/motifcounter., [email protected] , are available at bioinformatics online., transcription factors (tfs) play an essential role in the regulation […]

PMCID: 4595603
PMID: 26382656
DOI: 10.1038/ncomms9189

[…] bam files using samtools. bam files from different worm strains were analysed for reads predicted to derive from within telomeres using previously described software (http://sourceforge.net/projects/motifcounter/). briefly, reads that contained at least six canonical telomere repeats (ttaggc) were extracted and saved into separate files. the number of reads was counted and normalized to total […]

PMCID: 3919612
PMID: 24225324
DOI: 10.1093/nar/gkt1117

[…] (hg18) using burrows–wheeler alignment tool (). sequence reads were 100 nt. the telomeric subset of reads was extracted using a previously reported custom script (http://sourceforge.net/projects/motifcounter/) () incorporating functions from samtools () and standard linux pattern-matching programs. genome coverage was calculated using bedtools. telomere counts were normalized to genome […]


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motifcounter institution(s)
Max Planck Institute for molecular Genetics, Berlin, Germany
motifcounter funding source(s)
Supported by the IMPRS-CBCS.

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