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)

Citation