Man page - bedextract(1)
Packages contains this manual
- starchcluster_sge(1)
- bedmap(1)
- bedops-starch(1)
- bam2bed(1)
- starchstrip(1)
- bam2bed_slurm(1)
- gff2bed(1)
- bam2starch_slurm(1)
- gtf2starch(1)
- bam2starch_sge(1)
- psl2bed(1)
- psl2starch(1)
- vcf2starch(1)
- closest-features(1)
- bedops(1)
- bedextract(1)
- gtf2bed(1)
- sort-bed(1)
- wig2bed(1)
- bam2bed_sge(1)
- sam2starch(1)
- gvf2bed(1)
- gvf2starch(1)
- sam2bed(1)
- rmsk2starch(1)
- bam2starch(1)
- unstarch(1)
- gff2starch(1)
- starchcluster_slurm(1)
- starchcat(1)
- rmsk2bed(1)
- convert2bed(1)
- vcf2bed(1)
- wig2starch(1)
apt-get install bedops
Manual
BEDEXTRACT
NAMEDESCRIPTION
SEE ALSO
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.