Identifies the genomic locations of restriction sites.

usage: hicFindRestSite --fasta mm10.fa --searchPattern AAGCTT -o rest_site_positions.bed

Required arguments

--fasta, -f

Path to fasta file for the organism genome.

--searchPattern, -p

Search pattern. For example, for HindIII this pattern is “AAGCTT”. Both, forward and reverse strand are searched for a match. The pattern is a regexp and can contain regexp specif syntax (see https://docs.python.org/2/library/re.html). For example the patternCG..GC will find all occurrence of CG followed by any two bases and then GC.

--outFile, -o

Name for the resulting bed file.

Optional arguments


show program’s version number and exit

Further usage

In case multiple restriction enzymes are used in one experiment, hicFindRestSite can be used to find restriction sites individually per enzyme. Afterwards, all output bed files should be combined. However, it should be noted that the QC report will not be correct for this specific usage.