CIRI protocols

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CIRI specifications

Information


Unique identifier OMICS_09198
Name CIRI
Alternative name CIRI2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, SAM, GFT
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Version 2.0.6
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Fangqing Zhao <>

Publications for CIRI

CIRI in pipelines

 (9)
2018
PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522

[…] events was performed by considering reads paired with each bs spanning read. the genomic coordinates of these reads were retrieved from bwa alignment outputs using bs read identifiers provided by ciri. then, the reads genomic coordinates were mapped against ensembl exon genomic coordinates. only perfectly matched reads were considered for this analysis., alu annotations were downloaded […]

2018
PMCID: 5867839
PMID: 29495353
DOI: 10.3390/genes9030118

[…] with default settings []. the 19mb genome sequence of c. neoformans jec21 consists of 14 chromosomes with different lengths changing from 762 kilobase (kb) pairs to 2.3 megabase (mb) pairs. , the ciri algorithm (version 1.2) was the tool to identify circrnas in c. neoformans jec21 []. ciri was performed with default options, with the computer command: ciri_v1.2.pl -i input.sam -o […]

2017
PMCID: 5366334
PMID: 28396678
DOI: 10.3389/fpls.2017.00413

[…] kiwifruit actin (achn107181) as endogenous control genes., to compare the expression of circrnas across various kiwifruit tissues and taxa, we calculated the accounts of backspliced reads from the ciri results for each circrna that was normalized by using the total sequencing reads in a corresponding sample data set (defined as reads per million mapped reads, rpm) as an indicator […]

2017
PMCID: 5561264
PMID: 28819222
DOI: 10.1038/s41598-017-08806-0

[…] from the sequencing raw data using trimmomatic (version 0.32) (parameters: illuminaclip: adaptor.fa:2:30:10 leading:3 trailing:3 slidingwindow:4:15 minlen:50). the software segemehl (v 0.1.7) and ciri (v 2.0.5) were used for potential back-splice sites extraction, ., total rna was isolated by trizol reagent (life technologies, carlsbad, ca) followed by dna residue depletion using dnase […]

2017
PMCID: 5698953
PMID: 29162050
DOI: 10.1186/s12864-017-4304-3

[…] the examined characteristic and fdr values were determined using a benjamini and hochberg correction. roc analysis was performed using proc (v1.10.0) []., trimmed reads were also used as input for ciri2 [, ] to identify circrnas that mapped to annotated splice sites. a circrna junction scaffold of 170 nts in length (85 nts of the downstream exonic junction and 85 nts of the upstream exonic […]


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CIRI in publications

 (31)
PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] from astrocytes microdissected from the posterior cingulate (pc) of alzheimer’s disease (ad) patients (n = 10) and healthy elderly controls (n = 10) using four circrna prediction algorithms - ciri, circexplorer, find_circ and knife., overall, utilizing these four tools, we identified a union of 4438 unique circrnas across all samples, of which 70.3% were derived from exonic regions. […]

PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020

[…] was published (zeng et al., ), and we previously analyzed and compared the output from 5 different algorithms (hansen et al., ): circrna_finder (westholm et al., ), circexplorer (zhang et al., ), ciri (gao et al., ), find_circ (memczak et al., ), and mapsplice (wang et al., ). here, this analysis is extended by 6 additional algorithms: acsf (you et al., ), circexplorer2 (zhang et al., ), […]

PMCID: 5867839
PMID: 29495353
DOI: 10.3390/genes9030118

[…] adaptors and filtering low-quality reads, we obtained 39.28 million clean reads (). , clean reads were then mapped to the c. neoformans jec21 genome by bwa software. the mapped reads were input to ciri, a published circrna identifier, to identify the candidates of circrnas. to reduce false-positive candidates, the circrnas that had more than one back-splicing junction read were considered. […]

PMCID: 5913670
PMID: 29474580
DOI: 10.1093/molbev/msy022

[…] transcripts were identified based on 58 circrna data including four human pfc samples generated in this study and 54 published circrna sequencing data (, online). circrnas were identified using ciri (). briefly, the raw circrna sequencing data were mapped to the human genome (hg19) using bwa-mem () with default parameters except “-t 19” (filters out alignments with score < 19), […]

PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522

[…] poly(a-) preparations from mcf-7 cells cultured in four different culture conditions, each in triplicate, obtained in our laboratory (materials and methods). the rna-seq data were analyzed using the ciri algorithm []. among 14,624 circrnas predicted by ciri, 3,271 candidate circrnas were selected after the application of several filters (materials and methods). the final set of 3,271 circrnas, […]


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CIRI institution(s)
Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
CIRI funding source(s)
The National Natural Science Foundation of China (grant numbers 91640117 and 91531306), the National Key R&D Program (grant number 2016YFC1200804) and the Strategic Priority Research Program of the Chinese Academy of Sciences (grant number XDB13000000).

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