REforge

REforge (Regulatory Element forward genomics) is a method to associate transciption factor binding site divergence in regulatory elements with phenotypic differences between species [1].

Requirements:

• Python3 with Bio and rpy2 (requires R)
• Stubb_2.1 [2]
• tree_doctor [3]. A linux 64 bit binary is included. The source code is available at https://github.com/CshlSiepelLab/phast/ in src/util/

Installation:

git clone https://github.com/hillerlab/REforge

Download Stubb (http://www.sinhalab.net/software) and newmat11 (http://www.robertnz.net/download.html)

cp /path/to/stubb_2.1.tar.gz /path/to/newmat11.tar.gz .
tar -xvf stubb_2.1.tar.gz
tar -xvf newmat11.tar.gz -C stubb_2.1/lib/newmat/

# REforge uses a slightly modified version of Stubb
cd stubb_2.1/
patch -p1 < /path/to/REforge/stubb.patch
cd lib/newmat/
gmake -f nm_gnu.mak
cd ../../
make
export PATH=$PATH:`pwd`/bin
cd /path/to/REforge/
export PATH=$PATH:`pwd`

Example of screening 55 simulated CREs

# this directory contains a minimal example of simulated CREs
cd example

# Create a joblist file 'alljobs_simulation' containing the branch_scoring jobs
REforge.py data/tree_simulation.nwk data/motifs.wtmx data/species_lost_simulation.txt elements_simul.ls \
  --windowsize 200 --scorefile scores_simulation -bg=background/

# Run job list as batch or in parallel 
bash alljobs_scores_simulation > scores_simulation

# Run the association test
REforge_statistics.py data/tree_simulation.nwk data/motifs.wtmx data/species_lost_simulation.txt \
   elements_simul.ls --scorefile scores_simulation
# This generates a file 'significant_elements_simulation' that alphabetically lists the elements, their P-value and the number of branches

General workflow

Input data

• species tree in newick format
• motif file in wtmx format (see example/data/motifs.wtmx as example) listing all motifs, each according to the following model:

>motif_name motif_length [optional fields]
pos1_freqA pos1_freqC pos1_freqG pos1_freqT
pos2_freqA pos2_freqC pos2_freqG pos2_freqT
..
posN_freqA posN_freqC posN_freqG posN_freqT
<

• Phenotype-loss species list: one species per line (see example/data/species_lost_simulation.txt)
• CRE fastafiles: each file contains the sequence for every (ancestral or extant) species
• CRE list: path of fastafile of one CRE per line

Step 1: Branch score computation

Generate the REforge branch_scoring commands for all CREs.

REforge.py <tree> <motiffile> <lost_species_list> <element_list>

This creates for every CRE a REforge_branch_scoring.py job. Each line in alljobs_<scorefile> consists a single job. Each job is completely independent of any other job, thus each job can be run in parallel to others.

Execute that alljobs file. Either sequentially via

bash alljobs_simulation > scores_simulation

or run it in parallel by using a compute cluster. Every job returns a line in the following format:

motif_file CRE_file (branch_start>branch_end:branch_score )* <

which should be concatenated into a file called "<scorefile>".

Step 2: Association test

REforge_statistics.py <tree> <motiffile> <lost_species_list> <element_list>

REforge_statistics.py classifies branches into trait-loss and trait-preserving and assesses the significance the association of this classification with the branch scores.

Common Parameters

REforge.py

--scorefile <name>
Name file <name> instead of "scores"
--windowsize/-w <n>
Scoring window used in sequence scoring
--background/-bg <folder>
Background used for sequence scoring. Either a file or a folder structure with backgrounds for different GC contents
--scrCrrIter <n>
Stubb score is corrected with the average score of <number> of shuffled sequences. Default is 10. 0 turns the score correction off

REforge_statistics.py

--scorefile <name>
Use <name> as scorefile instead of "scores"
--filterspecies <comma separated list>
Exclude species from analyses
--elements <file>
Analyse only the elements specified <file>

Special parameters

--verbose/-v
--debug/-d

REforge.py

--no_ancestral_filter
Turn of ancestral score filtering
--no_branch_filter
Turn of branch score filtering
--no_fixed_TP
Do not fix transition probabilites while computing branch scores
--filter_branch_threshold <x>
Threshold for branch filter; By default branches are filtered if start and end node score are below 0
--filter_GC_change <x>
Filter branches with a GC content change above <x>
--filter_length_change <x>
Filter branches with a relative length change above <x>

References

[1] Langer BE, Roscito JG, Hiller M. REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species.

[2] Sinha S, van Nimwegen E, Siggia ED. A Probabilistic Method to Detect Regulatory Modules. Bioinformatics, 19(S1), 2003

[3] Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: Phylogenetic Analysis with Space/Time Models. Briefings in Bioinfomatics 12(1):41-51, 2011.