findRestSites¶
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 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. |