8. CpG_logo.py

8.1. 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.

8.2. 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.

8.3. Input files (examples)

• Human reference genome sequences in FASTA format: hg19.fa.gz and hg38.fa.gz
• 450_CH.hg19.bed.gz

8.4. Command

$CpG_logo.py -i 450_CH.hg19.bed.gz -r hg19.fa -o 450_CH

8.5. 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