Paraclu protocols

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Paraclu specifications


Unique identifier OMICS_21177
Name Paraclu
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 9.0
Stability Stable
a C++ compiler.
Source code URL
Maintained Yes



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  • person_outline Martin Frith <>
  • person_outline Albin Sandelin <>
  • person_outline Paraclu Team <>

Additional information

Publication for Paraclu

Paraclu in pipelines

PMCID: 5930951
PMID: 29716548
DOI: 10.1186/s12864-018-4692-z

[…] generated per library). the sequencing data was analyzed using fastqc (, filtered using tagdust2 [], mapped using bwa [], clustered using paraclu [], and visualized using bedtools [] and the ucsc genome browser []., rsox-4 was lr cloned upstream of a lacz reporter gene directed by the hsp68 minimal promoter []. the plasmid was sequence […]

PMCID: 4613594
PMID: 25664506
DOI: 10.4161/15384101.2014.988031

[…] over 10 and therefore mapping to single loci in the genomes were used in our analyses. subsequently, reads mapping to rdna were eliminated. cage tag 5′ genomic coordinates were used as input for paraclu clustering with the following parameters: (i) a minimum of 5 tags per cluster, (ii) maximum density/baseline density ≥2 and (iii) a maximal cluster length of 200 bp., annotation of cage tag […]

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Paraclu in publications

PMCID: 5677018
PMID: 29116076
DOI: 10.1038/s41467-017-01467-7

[…] enhancer elements characterized with bidirectional transcription patterns in our samples were selected. to this end, we first produced cage tag clusters using the paraclu method (v9), with cage tag 5′ genomic coordinates as input and (i) a minimum of five tags per cluster, (ii) a (maximum density)/(baseline density) ≥ 2 and (iii) a maximal cluster length […]

PMCID: 5597620
PMID: 28904364
DOI: 10.1038/s41598-017-11574-6

[…] version hg19. samtools was used to convert alignment files between sam and bed formats. overlapping reads, or cage initial transcription start sites (ctss), were clustered into tag clusters (tc) by paraclu v.9. read counts were normalized to tags per million (tpm). ctss with less than 0.1 tpm were excluded from the clustering step. tcs with <30 counts or length >200 bps were also […]

PMCID: 5110153
PMID: 27681123
DOI: 10.1128/JVI.01625-16

[…] to the 5′ end in the reverse transcription process (). to correct one base shift of the 5′ end, the first mismatched g was removed. we then clustered the tags to define distinct cage peaks using paraclu with the following parameters: (i) a minimum of 100 total tags per cluster, (ii) a minimum density increase of 2, and (iii) a maximal cluster length of 100 bp (). paraclu was designed […]

PMCID: 5062983
PMID: 27407110
DOI: 10.1093/nar/gkw629

[…] of smrt circular consensus sequence reads starting at each coordinate) averages of the start coordinates of cfls within the cluster., start site clusters in mapped deepcage data were extracted using paraclu () with the parameters (i) a minimum of 15 tags/cluster, (ii) (maximum density/baseline density) ≥ 2 and (iii) 1–20 base cluster length. consensus transcription start sites were determined […]

PMCID: 4466890
PMID: 26073445
DOI: 10.1038/srep11136

[…] across all group samples to the group average gene expression)., to define tss positions, cage tags belonging to each sample were clustered using an iterative hierarchical clustering approach with paraclu v9 to form clusters covering regions of less than 50 bp (). clusters that were more than 50 bp in length or were represented by fewer than 5 tags after rescaling were removed. clusters […]

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Paraclu institution(s)
Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Kanagawa, Japan; ARC Centre in Bioinformatics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; The Bioinformatics Centre, Department of Molecular Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes, Denmark; Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Saitama, Japan
Paraclu funding source(s)
Supported by a Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government; a grant of the Genome Network Project from the Ministry of Education, Culture, Sports, Science, and Technology, Japan; the Strategic Programs for R&D of RIKEN Grant for the RIKEN Frontier Research System, Functional RNA research program; and a grant from the Novo Nordisk Foundation to the Bioinformatics Centre.

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