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 replicating 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 makes Repliscan generally applicable and superior to previous methods with thresholds inapplicable to different genomes.
Conclusions Repliscan is simple and effective to use on organisms with different magnitude genome sizes and sequencing coverage as low as 2.4x.
List of Abbreviations
- TimEx
- Time of replication
- Repli-seq
- Replication label incorporation sequencing
- Edu
- 5-Ethynyl-2’-deoxyuridine
- BrdU
- 5-Bromo-2’-deoxyuridine
- NGS
- Next generation sequencing
- SRA
- Sequence read archive
- G1
- Gap 1 of cell division
- G2
- Gap 2 of cell division
- S
- Synthesis phase of cell division
- E
- Early S-phase replication
- M
- Middle S-phase replication
- L
- Late S-phase replication
- WB
- Whisker bounds