NAME
bedextract - manual page for bedextract 2.4.41+dfsg
DESCRIPTION
bedextract
-
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-
https://doi.org/10.1093/bioinformatics/bts277
- version:
-
2.4.41 (typical)
- authors:
-
Shane Neph & Alex Reynolds
-
Every input file must be sorted per sort-bed.
-
USAGE:
- 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.
SEE ALSO
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.