PT  - JOURNAL ARTICLE
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
TI  - Repliscan: a tool for classifying replication timing regions
AID  - 10.1101/094177
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 094177
4099  - http://biorxiv.org/content/early/2017/01/29/094177.short
4100  - http://biorxiv.org/content/early/2017/01/29/094177.full
AB  - 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.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