Deprecated: Please use alfred replication which is available here.
git clone --recursive https://github.com/tobiasrausch/repliseq.git
cd repliseq
make all
The order of bam files on the command line must follow the cell-cycle.
./src/repliseq -r <ref.fa> -o outprefix <g1b.bam> <s1.bam> <s2.bam> <s3.bam> <s4.bam> <g2.bam>
Plotting tag densities for each cell-cycle fraction.
Rscript R/reppattern.R -f outprefix.profile.tsv -r chr12:24000000-26000000
Plotting the replication time.
Rscript R/reptime.R -f outprefix.reptime.tsv -r chr12