MocoLoco aims to identify positionally-constrained conserved motifs within the genomic regions surrounding TF binding sites identified through ChIP-Seq or similar assays.
If you want to know how the tool works: MocoLoco_REPORT.
g++ -Wall -o MOCO MocoLoco.cpp -lgsl -lgslcblas -O3
The current stable version of GSL is always available from ftp.gnu.org in the directory /pub/gnu/gsl.
A list of mirror sites can be found at http://www.gnu.org/order/ftp.html
The project homepage is http://www.gnu.org/software/gsl/
./MOCO -b <file.bed> -p <number>(optional) -t <file.2bit> -j <file.JASPAR> -k <number, number, ...>(optional) -d <number, number, ...>(optional) -o p(optional) -e <number>(optional) -f <number, number, ...>(optional) -s(optional) -u(optional) -l(optional) -z <number>(optional) -r <number>(optional)
./MOCO -m <file_multifasta.fa> -p <number>(optional) -k <number, number, ...>(optional) -d <number, number, ...>(optional) -o p(optional) -e <number>(optional) -f <number, number, ...>(optional) -s(optional) -l(optional) -z <number>(optional) -r <number>(optional)| Option | Parameter | Description |
|---|---|---|
| -b | --bed | Input bed file |
| -m | --mf | Input multifasta file |
| -t | --twobit | It is used with bed file to know from which genome extract the sequences |
| -j | --jaspar | Specify the jaspar file used as primary motif (used only if bed file as input file) |
| -k | --kmer | Length of k-mers in the analysis (DEFAULT: 6,8,10) |
| -d | --distance | It refers to the Hamming distance for the creation of oligos cluster (DEFAULT: 1,2,3) |
| -p | --param | It is the half-length of the sequences (DEFAULT: 150) |
| -s | --ss | To run the anlysis as single strand (DEFAULT: double strand) |
| -o | --ordering | It defines if the best oligos are ordered by pvalue (-o p) or by occurrences (DEFAULT) |
| -f | --freq | Set the frequence treshold to calculate the Zscore |
| -e | --exp_max | Refine the PWM matrices using the expectation maximization algorithm |
| -l | --tomtom | Set the output format suitable for Tomtom from MEME |
| -u | --unidirection | It orders the sequences in the same direction |
| -r | --secondary | Set how secondary matrices I need in the analysis |
| -z | --z_pval_threshold | Set the Zscore p-value threshold for eventually secondary matrices |
| -a | --cleaning | Disable the cleaning of sequences with low primary motif scores (DEFAULT: ON) |
This script uses the twobit.c and twobit.h file from this repository, you can find these files in TwoBit folder.
In this repository there are some useful folders for the usage of MocoLoco:
- Genomes where there are some TwoBit files of most important genomes
- Jaspar_2020 contains most of the matrices present in Jaspar database
- Test_Bed is a folder with some bed files from ENCODE that can be used as test files
- Random_multifa_TOOL contains an important tool used during MocoLoco testing, this tool is explained in the next chapter.
- TESTING_MOCOLOCO is a folder with some bash scripts used during MocoLoco testing.
It is a tool able to generate multifasta files with user-defined TFBSs motifs implanted at specific positions.
g++ -o RMC Multifa_random_tool.cpp
./RMC -j <JASPAR_FILE_1> <JASPAR_FILE_2> ... <JASPAR_FILE_N> -p <number, number, ....> -l <number> -n <number> -o <number, number,...> -w <number, number,...> -c <number> -f <number, number,..> ./RMC -l <number> -n <number> -c <number> | Option | Parameter | Description |
|---|---|---|
| -j | --jaspar | Specify the jaspar file used as primary motif for implants |
| -l | --length | Length of Multifasta sequences (DEFAULT: 500) |
| -n | --nseq | Number of Multifasta sequences (DEFAULT: 200) |
| -o | --oligop | Percentage of sequences in which the oligos will be implanted (DEFAULT: 0%) |
| -p | --position | Position of the implants in the sequences |
| -w | --wobble | The implanting position, for every oligo, will be randomly choosen between p-w and p+w interval (DEFAULT: 0) |
| -c | --cycles | How many random multifasta files this tool will produce (DEFAULT: 1) |
| -f | --freq | Percentage of fwd/rev strand to select for the implants. (DEFAULT: 50) |