bedextract - manual page for bedextract 2.4.35+dfsg
- 2.4.35 (typical)
- Shane Neph & Alex Reynolds
- Every input file must be sorted per sort-bed.
- 0) --help or --version
- Print requested info and exit successfully
- 1) --list-chr <input.bed>
- Print all unique chromosome names found in <input.bed>
- 2) <chromosome> <input.bed>
- Retrieve all rows for chr8 with: bedextract chr8 <input.bed>
- 3) <query.bed> <target>
- Grab elements from the <query.bed> that overlap elements in
<target>. Same as
- `bedops -e 1 <query.bed> <target>`, except that this
option fails silently
- if <query.bed> contains fully-nested BED elements. If no
fully-nested element exists, bedextract can vastly improve upon the
performance of bedops. <target> may be a BED or Starch file (with or
without fully-nested elements). Using '-' for <target> indicates
input (in BED format) comes from stdin.
The full documentation for bedextract is maintained as a Texinfo manual.
If the info and bedextract programs are properly installed at
your site, the command
- info bedextract
should give you access to the complete manual.