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Quickstart
To check out all usage instructions available for GRAFIMO type
grafimo --help # or grafimo -h
Scannig a genome variation graph (built constructing graph for each chromosome) for the occurrences of a DNA motif in a set of genomic regions defined in a BED file. Note that the motif(s) can be given in MEME or JASPAR format.
grafimo -d /path/to/directory/stroring/my/graphs/ -b /path/to/my/bedfile -m path/to/my/motif
Scanning a whole genome graph for the occurrences of a DNA motif in a set of genomic regions defined in a BED file. Note that the motif(s) can be given in MEME or JASPAR format.
grafimo -g /path/to/my/whole/genome/vg -b /path/to/my/bedfile -m /path/to/my/motif
Building the genome variation graph with GRAFIMO (GRAFIMO will build a graph for each single chromosome). Note that the names of chromosomes must be identical on both the reference genome and the VCF file containing the genomic variants; for example if in the VCF the chromosome 1 is named as 1
, the reference genome FASTA file must contain >1
instead of >chr1
in chromosome 1 sequence header.
grafimo buildvg -l /path/to/reference/genome -v /path/to/vcf/file