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Protocols

RECLU specifications

Information


Unique identifier OMICS_07114
Name RECLU
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
Requirements
SAMtools, BEDtools
Maintained Yes

Versioning


No version available

Publication for RECLU

RECLU citations

 (4)
library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

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

2016
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 […]

call_split

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

2015
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 (http://cell-innovation.nig.ac.jp/wiki2/tiki-index.php?page=p000001286), integrated into maser (national institute of genetics; https://cell-innovation.nig.ac.jp/index_en.html) […]


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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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