CEMIG (Cis rEgulatory Motif Influence using de Bruijn Graph)
CEMIG is a new motif prediction algorithm which takes k-mer as the basic unit, finds motif seeds by introducing hash table and describing the relationship between k-mers constituting motif by using de Bruijn graph model, and then merges and extends among motif seeds, so as to more accurately predict the transcriptional motifs in ATAC-seq data.
Prerequisites and Dependencies
- C++11
- bedtools
Motif Prediction
cd code/
./cemig -i test.fa
| Arguments | Description |
|---|---|
| --InputFile(-I) | Input file with standard FASTA file format in default |
| --GenomeFile(-G) | Genome files with standard FASTA file format |
| --OutFileNamePrefix(-O) | Number of flanking base pairs at each side of peak summit (default is 50) |
| --Paired-end(-P) | Whether the input data is paired-end (true in defalut) |
| --MaxMotifs | Maximum number of output motifs (100 in default) |