These are scripts for calculating replication timing, fork velocity per gene and origin mapping for WT strains shown in Supplemental-Figures S10 and S11
Start with processed data file WT_all_readsFandR_norm_50bp_Fig_S8BGEO.txt from GSE160509
Proceed with scripts in the following order (you will need to change the directory names and input and output file names in the script and write shell scripts for job submission to your computing cluster)
Replication Timing:
1.normalize_to_input-wholegenome_notlog2.pl
2.normto1perchafternormtoinptFRseparate.pl
3.normto1perchafternormtoinptsepFRcleanupwmovavg400bp.pl
4.find_rep_time_from_timecourse_400bpbins_newv3withmaxperline-FRsep.pl ; this script calculates replication timing as described in Data Analysis- Replication Timing  section of Supplemental Methods.
5.reptimesigmoidmovingavg50bprtbins_FRsep.pl
6.add_rep-timesigmoid081119WT_to_solexa_reads_annot_together_FRsep.pl
Origin mapping (uses the 18min and the 25min time points from the input time course above):
7.find_peaks3binsbp_FRsep.pl
8.isolate_Repl_Origin_Assoc_Domainsbins.pl
9.newARS081119WT_from_EdU_RADreptimesigmoid-oridbars.pl
10.put_together_newARS.pl
11.put_together_newARSfrom25min.pl
12.ARS_alignment18min.pl
13.ARS_alignment25min.pl
14.find_peaks2_peralignedARS18min.pl
15.find_peaks2_peralignedARS25min.pl
16. use outputs from 14 and 15, and take out columns 2,3,and 8 (columns start with 0) and filter out rows with replication timing of 0min or ND in Excel to generate input for retrieve_ARSseq.pl and retrieve_25minARSseq.pl
17. closest_ACS_toNChAPpeak.pl and closest_25minACS_NChAPpeak.pl
18.find_closest_newARS081119WT_18minNCHAPFRwACSaligned_to_EdU_RAD2.pl
19.find_closest_newARS081119WT_25minNCHAPFRwACSaligned_to_EdU_RAD2.pl
20.groupROADaroundclosestnewARS081119WT_18minNCHAPFRwACSaligned.pl and groupROADaroundclosestnewARS081119WT_25minNCHAPFRwACSaligned.pl
Fork Velocity:
21.linearfitwintercept0_forkvelocitypergene_from_timecoursearsaligned_sepFR.pl ; this script calculates DNA synthesis rates per gene as described in Data Analysis- DNA synthesis rates section of Supplemental Methods.
22.linearfitwintercept0_forkvelocitypergene_from_timecoursearsalignedtogether_FRsep.pl
23.lagversusleadforkvelocity.pl

