Identifies the genomic locations of restriction sites.

usage: findRestSite --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 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