Mango: a bias-correcting ChIA-PET analysis pipeline.
Bioinformatics
; 31(19): 3092-8, 2015 Oct 01.
Article
en En
| MEDLINE
| ID: mdl-26034063
ABSTRACT
MOTIVATION Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity. RESULTS:
Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs. AVAILABILITY AND IMPLEMENTATION Mango is open source and distributed through github at https//github.com/dphansti/mango. CONTACT mpsnyder@standford.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Bases de datos:
MEDLINE
Asunto principal:
Programas Informáticos
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Estadística como Asunto
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Análisis de Secuencia de ADN
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Inmunoprecipitación de Cromatina
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2015
Tipo del documento:
Article