Hostname: x2-08-1.genome.duke.edu
Slurm Array Index:
Time Stamp: 09-24-24+17:39:49
Input: /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results/region/fcc_astarr_macs/K562.hg38.ASTARR.macs.KS91.input.rep_all.max_overlaps.q5.bed.gz
show first few lines of input
chr1 10038 10405
chr1 14282 14614
chr1 16025 16338
chr1 17288 17689
chr1 28934 29499
chr1 115429 115969
chr1 136201 137353
chr1 137748 138049
chr1 138321 139517
chr1 181005 181854
bedtools is a powerful toolset for genome arithmetic.
Version: v2.31.1
About: developed in the quinlanlab.org and by many contributors worldwide.
Docs: http://bedtools.readthedocs.io/
Code: https://github.com/arq5x/bedtools2
Mail: https://groups.google.com/forum/#!forum/bedtools-discuss
Usage: bedtools <subcommand> [options]
The bedtools sub-commands include:
[ Genome arithmetic ]
intersect Find overlapping intervals in various ways.
window Find overlapping intervals within a window around an interval.
closest Find the closest, potentially non-overlapping interval.
coverage Compute the coverage over defined intervals.
map Apply a function to a column for each overlapping interval.
genomecov Compute the coverage over an entire genome.
merge Combine overlapping/nearby intervals into a single interval.
cluster Cluster (but don't merge) overlapping/nearby intervals.
complement Extract intervals _not_ represented by an interval file.
shift Adjust the position of intervals.
subtract Remove intervals based on overlaps b/w two files.
slop Adjust the size of intervals.
flank Create new intervals from the flanks of existing intervals.
sort Order the intervals in a file.
random Generate random intervals in a genome.
shuffle Randomly redistribute intervals in a genome.
sample Sample random records from file using reservoir sampling.
spacing Report the gap lengths between intervals in a file.
annotate Annotate coverage of features from multiple files.
[ Multi-way file comparisons ]
multiinter Identifies common intervals among multiple interval files.
unionbedg Combines coverage intervals from multiple BEDGRAPH files.
[ Paired-end manipulation ]
pairtobed Find pairs that overlap intervals in various ways.
pairtopair Find pairs that overlap other pairs in various ways.
[ Format conversion ]
bamtobed Convert BAM alignments to BED (& other) formats.
bedtobam Convert intervals to BAM records.
bamtofastq Convert BAM records to FASTQ records.
bedpetobam Convert BEDPE intervals to BAM records.
bed12tobed6 Breaks BED12 intervals into discrete BED6 intervals.
[ Fasta manipulation ]
getfasta Use intervals to extract sequences from a FASTA file.
maskfasta Use intervals to mask sequences from a FASTA file.
nuc Profile the nucleotide content of intervals in a FASTA file.
[ BAM focused tools ]
multicov Counts coverage from multiple BAMs at specific intervals.
tag Tag BAM alignments based on overlaps with interval files.
[ Statistical relationships ]
jaccard Calculate the Jaccard statistic b/w two sets of intervals.
reldist Calculate the distribution of relative distances b/w two files.
fisher Calculate Fisher statistic b/w two feature files.
[ Miscellaneous tools ]
overlap Computes the amount of overlap from two intervals.
igv Create an IGV snapshot batch script.
links Create a HTML page of links to UCSC locations.
makewindows Make interval "windows" across a genome.
groupby Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
expand Replicate lines based on lists of values in columns.
split Split a file into multiple files with equal records or base pairs.
summary Statistical summary of intervals in a file.
[ General Parameters ]
--cram-ref Reference used by a CRAM input
[ General help ]
--help Print this help menu.
--version What version of bedtools are you using?.
--contact Feature requests, bugs, mailing lists, etc.
Done!
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