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- Title
Repliscan: a tool for classifying replication timing regions.
- Authors
Zynda, Gregory J.; Jawon Song; Concia, Lorenzo; Wear, Emily E.; Hanley-Bowdoin, Linda; Thompson, William F.; Vaughn, Matthew W.
- 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.
- Subjects
DNA replication; NUCLEOTIDE sequencing; DNA analysis; ARABIDOPSIS thaliana; PLANT genomes; COMPUTER software
- Publication
BMC Bioinformatics, 2017, Vol 18, p1
- ISSN
1471-2105
- Publication type
Article
- DOI
10.1186/s12859-017-1774-x