Sailfish-cir protocols

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Sailfish-cir specifications

Information


Unique identifier OMICS_16651
Name Sailfish-cir
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.11
Stability Alpha
Requirements
cufflinks, sailfish, gffutils
Maintained Yes

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Maintainer


  • person_outline Wanjun Gu <>

Publication for Sailfish-cir

Sailfish-cir in pipeline

2017
PMCID: 5828303
PMID: 29248507
DOI: 10.1016/j.ebiom.2017.12.007

[…] we quantified the expression values of all identified circular transcripts and known linear transcripts in the ensembl () human gene annotation (release 87) using our recent developed tool, sailfish-cir (), with default settings. for each host gene, the transcripts per million (tpm) values of both linear and circular transcripts were recorded. these circrna identification […]


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Sailfish-cir in publication

PMCID: 5828303
PMID: 29248507
DOI: 10.1016/j.ebiom.2017.12.007

[…] we sequenced four rrna-depleted rna-seq libraries of human pbmc samples in the discovery cohort (supplementary table s3). the expression of both mrnas and circrnas was simultaneously quantified by sailfish-cir (). in total, 5175 parental genes were found to express circular transcripts in these four human pbmc samples, among which the circular transcripts of 131 parental genes were highly […]


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Sailfish-cir institution(s)
State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China; Research Center for Learning Sciences, Southeast University, Nanjing, Jiangsu, China; Department of Orthopedics and Trauma, Peking University People’s Hospital, Beijing, China; Department of Physiology and Cell Biology, The University of Nevada School of Medicine, Reno, NV, USA
Sailfish-cir funding source(s)
Supported by grants from National Basic Research Program of China (2012CB316501), National High Technology Research and Development Program of China (2012AA020401) and National Natural Science Foundation of China (61171143, 61471112 and 61571109, 61372164).

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