1. Repliscan: a tool for classifying replication timing regions.
- Author
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Zynda GJ, Song J, Concia L, Wear EE, Hanley-Bowdoin L, Thompson WF, and Vaughn MW
- Subjects
- Genome, Genome Size, DNA Replication Timing, High-Throughput Nucleotide Sequencing methods, Sequence Analysis, DNA methods, Software
- Abstract
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.
- Published
- 2017
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