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bedextract - manual page for bedextract 2.4.26+dfsg

BEDEXTRACT(1) User Commands BEDEXTRACT(1)

NAME

bedextract - manual page for bedextract 2.4.26+dfsg

DESCRIPTION

bedextract
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract version: 2.4.26 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.
June 2017 bedextract 2.4.26+dfsg