Examples¶

Small recipes that you can copy. All commands run from the repository root (python -m src.run ...) or after installation (replisage ...). Replace the data paths with your own.

The test region used in most examples is chr14:80835000-98674700, which is covered by the shipped single-cell replication timing (--rt-file builtin).

Command-line recipes¶

1. Loop extrusion only. The fastest run; no replication, no 3D.

replisage --bedpe-file loops.bedpe --region chr14:80835000-98674700

2. Add replication timing, Monte Carlo only. Replication is simulated, loops and compartments are sampled across G1, S and G2/M.

replisage --bedpe-file loops.bedpe --region chr14:80835000-98674700 --rt-file builtin --run-md false

3. Full 3D run on a GPU. Two sister chromatids, viewer and movie are written.

replisage --bedpe-file loops.bedpe --region chr14:80835000-98674700 --rt-file GM12878.bigWig \
          --run-md true --platform CUDA

4. Replication stress.

replisage --bedpe-file loops.bedpe --region chr14:80835000-98674700 --rt-file builtin --with-stress

5. Several replicas in parallel, for convergence checks.

replisage --bedpe-file loops.bedpe --region chr14:80835000-98674700 --n-replicas 4 --threads 4 --seed 1

6. A whole chromosome.

replisage --bedpe-file loops.bedpe --region chr14 --n-beads 2000

7. From a config file, with one flag changed.

replisage -c examples/replication_3d.ini --seed 5 --name seed5

Real data: GM12878 loops and Repli-seq¶

A CTCF ChIA-PET loop file and an ENCODE Repli-seq bigWig of GM12878, on a small 2 Mb region. The bigWig is log-transformed by default (BIGWIG_LOG_NORM = True in the config).

replisage --bedpe-file LHG0052H_loops_cleaned_th10_2.bedpe --rt-file ENCFF001GNK.bigWig \
          --region chr14:90000000-92000000 --n-beads 200 --run-md false --name gm12878_small

Annotated config files¶

File	Use case
`loops_only.ini`	Loop extrusion without replication
`replication_mc.ini`	Replication and compartments, Monte Carlo only
`replication_3d.ini`	Full cell cycle with 3D structures
`replication_stress.ini`	Slow forks, extra origins
`two_lef_families.ini`	Two kinds of extruders with different folding strength
`production_replicas.ini`	Long runs with several replicas

Edit the data paths at the top of each file before running.

Only a config file¶

If the file defines the input, -c is all you need:

[input]
bedpe_path = loops.bedpe
chrom = chr14
region_start = 80835000
region_end = 83835000
rept_path = builtin          ; a file, builtin or none
[mc]
preferential_binding = True
[md]
simulation_type = MD         ; none = no 3D

replisage -c my.ini

A 3 Mb region with 3D structures¶

Beads are set automatically (7 kb per bead gives about 430 beads):

replisage --bedpe-file loops.bedpe --region chr14:80835000-83835000 --rt-file builtin --run-md true --name chr14_3Mb_md