Program_Flow.md

Program flow

Introduction

This program flow is relative to running in standalone mode, running the script multiple_run_all.m inside an interative MATLAB session. For running on a cluster, submitting jobs via job_submit.sh, then the flow is the same, starting from when multiple_run_chromhl.m is run.

Initialisation

• The script multiple_run_<type>.m reads in all FASTA sequences using Read_FASTA_all.m and runs Driver.m to perform the main loop.

Main loop

• For each sequence provided in, Driver.m computes the binding maps using CalculateMap.m and outputs a MATLAB file containing the maps, and a text file for each individual profile.
• CalculateMap.m runs in four parts:

  1. SetDefaults.m sets parameter defaults.

  2. ParametersInitMicrodomain.m initialises the statistical weights, the initiation sites and the CTCF-occupied lattice units.

     • CalculateCTCFAffinity.m applies the TRAP algorithm (via PWM_affinity.m) on the sequence level, then takes the maximum affinity per lattice unit to give a lattice-based affinity.

     • CalculatePAX39Affinity.m applies the TRAP algorithm (via PWM_affinity.m) for PAX3 and PAX9 transcription factors, then smooths the affinity using a geometric mean over a 501-bp centred window.

     • Once affinities are computed per lattice unit, the lattice unit is set as heterochomatin initiation site if the lattice PAX3/9 affinity is above a threshold or as CTCF-bound if the lattice CTCF affinity is above a threshold.

  3. ConstantsInitMicrodomain.m fixes the transfer matrix dimension and enumerates lattice unit states.

  4. MapOfBindingCalc.m computes the binding map using PointOfMapOfBindingCalc.m, running along the lattice.

     • PointOfMapOfBindingCalc.m computes the HP1 binding probability, and the probability of each chromatin state at that point in the lattice.
       • MatrixInitMicrodomain.m computes the transfer matrix and its derivatives with respect to protein binding and chromatin state.

Outputs

• The outputs are a MATLAB MAT file containing the binding maps for each sequence in the input MAT file, and a fixed-format text file with the binding map per lattice unit.

Expected running time

• For the four 8000-bp sequences provided as demonstration, the calculation of all maps takes approximately 5 seconds on an Intel Core i7-8550U CPU with 8 GB RAM.

  • Output files https://github.com/TeifLab/ChromHL/blob/master/chrF.CTCF-only.txt, https://github.com/TeifLab/ChromHL/blob/master/chrF.null-null.txt, https://github.com/TeifLab/ChromHL/blob/master/chrF.one-PAX3.txt and https://github.com/TeifLab/ChromHL/blob/master/chrF.PAX3-fwd-rev.txt should be generated