RT Journal Article
SR Electronic
T1 Repliscan: a tool for classifying replication timing regions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 094177
DO 10.1101/094177
A1 Gregory J Zynda
A1 Jawon Song
A1 Lorenzo Concia
A1 Emily E Wear
A1 Linda Hanley-Bowdoin
A1 William F Thompson
A1 Matthew W Vaughn
YR 2016
UL http://biorxiv.org/content/early/2016/12/14/094177.abstract
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 archiveGiGap 1 of cell divisionG2Gap 2 of cell divisionSSynthesis phase of cell divisionEEarly S-phase replicationMMiddle S-phase replicationLLate S-phase replication