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RECLU specifications


Unique identifier OMICS_07114
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl, R, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
SAMtools, BEDtools
Maintained Yes


No version available

Publication for RECLU

RECLU citations


TSS Seq analysis of low pH induced gene expression in intercalated cells in the renal collecting duct

PMCID: 5578634
PMID: 28859164
DOI: 10.1371/journal.pone.0184185

[…] were mapped to rat reference genomes using the tophat2 software after discarding the ribosomal and non-a/c/g/t base-containing rnas []. for tag clustering, the cage-tag 5’-coordinates were input for reclu clustering, with a maximum irreproducible discovery rate (idr) of 0.1 and a minimum tags per million (tpm) value [], followed by differential expression and motif discovery analyses. the r […]


MicroRNA 140 mediates RB tumor suppressor function to control stem cell like activity through interleukin 6

PMCID: 5355146
PMID: 28099924
DOI: 10.18632/oncotarget.14681

[…] cage tags were mapped to the mouse mm9 genomes using bwa software (v0.5.9) after discarding ribosomal or non-a/c/g/t base-containing rnas. for tag clustering, cage-tag 5′ coordinates were input for reclu clustering, with a maxmum irreproducible discovery rate of (idr) 0.1 and minimum tags per million (tpm) value of 0.1 [, ], genes were filtered into the rb inactivation signature if their tpm […]


Sustained expression of MCP 1 by low wall shear stress loading concomitant with turbulent flow on endothelial cells of intracranial aneurysm

PMCID: 4862234
PMID: 27160403
DOI: 10.1186/s40478-016-0318-3

[…] enough for further analyses (table ). then, profiling differentially expressing genes (peaks in rna sequence mapped to the reference genome) between experimental groups was obtained by a pipeline, reclu []. here, the reclu pipeline extracted two types of clusters, top peaks and bottom ones []. briefly, top peaks or bottom ones represent the narrowest or broadest reproducible peaks in an rna […]


Tor Signaling Regulates Transcription of Amino Acid Permeases through a GATA Transcription Factor Gaf1 in Fission Yeast

PMCID: 4686964
PMID: 26689777
DOI: 10.1371/journal.pone.0144677
call_split See protocol

[…] respectively. the remaining reads were mapped to s. pombe reference genome using bwa []. cage read clustering, differential gene expression analysis and motif discovery were performed by reclu ver3.1 pipeline (, integrated into maser (national institute of genetics; […]

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RECLU institution(s)
RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Japan

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