7. CpG_logo.py¶
7.1. Description¶
This program generates a DNA motif logo for a given set of CpGs. To answer the question of “what is the genomic context for a given list of CpGs ?”. This program first extracts genomic sequences around C position, and then generate motif matrices include:
position frequency matrix (PFM)
position probability matrix (PPM)
position weight matrix (PWM)
MEME format matrix
Jaspar format matrix
It also generates motif logo using weblogo
Notes
input BED file must have strand information.
7.2. Options¶
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -i INPUT_FILE, --input_file=INPUT_FILE
BED file specifying the C position. This BED file should have at least six columns (Chrom, ChromStart, ChromeEnd, name, score, strand). Note: Must provide correct strand information. This file can be a regular text file or compressed file (.gz, .bz2).
- -r GENOME_FILE, --refgenome=GENOME_FILE
Reference genome seqeunces in FASTA format. Must be indexed using the samtools “faidx” command.
- -e EXTEND_SIZE, --extend=EXTEND_SIZE
Number of bases extended to up- and down-stream. default=5 (bp)
- -n MOTIF_NAME, --name=MOTIF_NAME
Motif name. default=motif
- -o OUT_FILE, --output=OUT_FILE
The prefix of the output file.
7.3. Input files (examples)¶
Human reference genome sequences in FASTA format: hg19.fa.gz and hg38.fa.gz
7.4. Command¶
$CpG_logo.py -i 450_CH.hg19.bed.gz -r hg19.fa -o 450_CH
7.5. Output files¶
450_CH.logo.fa
450_CH.logo.jaspar
450_CH.logo.meme
450_CH.logo.pfm
450_CH.logo.ppm
450_CH.logo.pwm
450_CH.logo.logo.pdf
