PeakXus statistics

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PeakXus specifications

Information


Unique identifier OMICS_12710
Name PeakXus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data PeakXus accepts unaligned reads in fastq-format and aligned reads as sorted and indexed bam-files. UMI-labels must be provided in a tab-separated file where the first column is the label identifier and the second column the actual sequence.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
Matplotlib, BioPython, NumPy, SciPy, Pysam, Samtools
Maintained Yes

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Documentation


Maintainer


  • person_outline Tuomo Hartonen <>

Publication for PeakXus

PeakXus in publication

PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] et al. () (ena accession erx986066). mapping and peak calling was done as in hartonen et al. (), briefly: alignment was done using bwa () against assembly grch37 and the peaks were called using peakxus (). five thousand highest scoring peaks were selected, and around the peak summits sequences of length 60 were extracted (blacklisted regions (), encode accession encff001tdo, and centromeres […]


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PeakXus institution(s)
Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
PeakXus funding source(s)
This work has been supported financially by the Academy of Finland (Finnish Center of Excellence Program 2012–2017, 250345, Personal Grant 274555) and the Integrative Life Sciences (ILS) Doctoral Program.

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