Piranha protocols

View Piranha computational protocol

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Associated diseases

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Piranha specifications

Information


Unique identifier OMICS_00568
Name Piranha
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.1
Stability Stable
Requirements
GNU scientific, BAMtools, GCC
Maintained Yes

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Maintainer


  • person_outline Andrew Smith <>

Publication for Piranha

Piranha in pipeline

2015
PMCID: 4643281
PMID: 25774828
DOI: 10.1038/ncomms7517

[…] '--read-mismatches 1 --read-gap-length 1 --read-edit-dist 1 --max-multihits 100 --b2-very-sensitive --transcriptome-max-hits 100 --no-coverage-search --no-novel-juncs'. peaks were called using piranha with a window size of 200bp. motifs were identified using the meme software suite., total rna was isolated from total mouse small intestinal epithelial cells from 3 m2rtta and 3 tre-msi2 mice […]


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Piranha in publications

 (13)
PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] of whether a binding event is merely a result of transcript abundance or a more specific interaction between the rbp and its target rna. several peak calling programs have been developed and include piranha [], clipper [], pipe-clip [], pyicos [] that work with all clip variants, and paralyzer [] and wavcluster that are specifically developed for par-clip analysis. for more details […]

PMCID: 5893854
PMID: 29670884
DOI: 10.3389/fmolb.2018.00027

[…] database consisted of datasets analyzed using 4 different softwares paralyzer (corcoran et al., ), cims (crosslinking induced mutation site) (moore et al., ), cits (weyn-vanhentenryck et al., ), and piranha (uren et al., )., these datasets comprise of positions of interaction of rna binding protein and rna target sites derived after par-clip (photoactivatable ribonucleoside enhanced crosslinking […]

PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] (polya binding protein) binds to polya tails of (m)rnas (). we analyzed bam files for rna rip-seq libraries generated from k562 and hela cellular lysates and with antibodies raised against pabp with piranha for confirmation of tfbitr polyadenylation (,) (). the distribution of starting peaks at candidate 3′ termini was analyzed with default parameters (./piranha rip.bam -o (output) -p (threshold […]

PMCID: 5740069
PMID: 29269732
DOI: 10.1038/s41467-017-02353-y

[…] indeed differentially expressed in this disease (kolmogorov–smirnoff test p-value of melanoma vs. other tumors <0.05; see heatmaps in fig. )., the celf1 rip-seq data was then analyzed with the piranha software to assign reads (peak calling) to 3′ utrs, 5′ utrs, introns or coding regions. this approach revealed a preference of celf1 for 3′ utr binding (fig. , left pie chart). sequence […]

PMCID: 5591525
PMID: 28886744
DOI: 10.1186/s13059-017-1298-8

[…] by the scientific community., we collected 327 clip-seq datasets generated from three technical approaches: par-clip, hits-clip, and eclip. the binding peaks of par-clip data were defined by piranha [] and paralyzer []; the binding peaks of hits-clip data were defined by piranha and cims [] (see detail in “methods”). we also downloaded the binding peaks of eclip data, defined by clipper […]


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Piranha institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

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