Repliscan: a tool for classifying replication timing regions.
BMC Bioinformatics
; 18(1): 362, 2017 Aug 07.
Article
em En
| MEDLINE
| ID: mdl-28784090
BACKGROUND: Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing. RESULTS: To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds. CONCLUSIONS: Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.
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Base de dados:
MEDLINE
Assunto principal:
Software
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Análise de Sequência de DNA
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Período de Replicação do DNA
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Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article