TY - JOUR T1 - Repliscan: a tool for classifying replication timing regions JF - bioRxiv DO - 10.1101/094177 SP - 094177 AU - Gregory J Zynda AU - Jawon Song AU - Lorenzo Concia AU - Emily E Wear AU - Linda Hanley-Bowdoin AU - William F Thompson AU - Matthew W Vaughn Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/12/094177.abstract N2 - 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 makes 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 magnitude genome sizes and sequencing coverage as low as 2.4x.TimExTime of replicationRepli-seqReplication label incorporation sequencingEdu5-Ethynyl-2’-deoxyuridineBrdU5-Bromo-2’-deoxyuridineNGSNext generation sequencingSRASequence read archiveG1Gap 1 of cell divisionG2Gap 2 of cell divisionSSynthesis phase of cell divisionEEarly S-phase replicationMMiddle S-phase replicationLLate S-phase replicationWBWhisker bounds ER -