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Repliscan: a tool for classifying replication timing regions.
- Source :
-
BMC bioinformatics [BMC Bioinformatics] 2017 Aug 07; Vol. 18 (1), pp. 362. Date of Electronic Publication: 2017 Aug 07. - Publication Year :
- 2017
-
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.<br />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.<br />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.
Details
- Language :
- English
- ISSN :
- 1471-2105
- Volume :
- 18
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- BMC bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 28784090
- Full Text :
- https://doi.org/10.1186/s12859-017-1774-x