Category
Generic
Usage
featureBits database table(s)
Manual
This tool is part of UCSC Genome Browser's utilities.
This will return the number of bits in all the tables anded together
Pipe warning: output goes to stderr.
Options:
-bed=output.bedPut intersection into bed format. Can use stdout.
-fa=output.fa Put sequence in intersection into .fa file
-faMerge For fa output merge overlapping features.
-minSize=N Minimum size to output (default 1)
-chrom=chrN Restrict to one chromosome
-chromSize=sizefile Read chrom sizes from file instead of database.
(chromInfo three column format)
-orOr tables together instead of anding them
-not Output negation of resulting bit set.
-countGaps Count gaps in denominator
-noRandomDon't include _random (or Un) chromosomes
-noHapDon't include _hap chromosomes
-dots=N Output dot every N chroms (scaffolds) processed
-minFeatureSize=n Don't include bits of the track that are smaller than
minFeatureSize, useful for differentiating between
alignment gaps and introns.
-bin=output.binPut bin counts in output file
-binSize=N Bin size for generating counts in bin file (default 500000)
-binOverlap=N Bin overlap for generating counts in bin file (default 250000)
-bedRegionIn=input.bed Read in a bed file for bin counts in specific regions
and write to bedRegionsOut
-bedRegionOut=output.bed Write a bed file of bin counts in specific regions
from bedRegionIn
-enrichment Calculates coverage and enrichment assuming first table
is reference gene track and second track something else
Enrichment is the amount of table1 that covers table2 vs. the
amount of table1 that covers the genome. It's how much denser
table1 is in table2 than it is genome-wide.
'-where=some sql pattern' Restrict to features matching some sql pattern
You can include a '!' before a table name to negate it.
Some table names can be followed by modifiers such as:
:exon:N Break into exons and add N to each end of each exon
:cds Break into coding exons
:intron:N Break into introns, remove N from each end
:utr5, :utr3 Break into 5' or 3' UTRs
:upstream:NConsider the region of N bases before region
:end:N Consider the region of N bases after region
:score:NConsider records with score >= N
:upstreamAll:NLike upstream, but doesn't filter out genes that
have txStart==cdsStart or txEnd==cdsEnd
:endAll:N Like end, but doesn't filter out genes that
have txStart==cdsStart or txEnd==cdsEnd
The tables can be bed, psl, or chain files, or a directory full of
such files as well as actual database tables. To count the bits
used in dir/chrN_something*.bed you'd do:
featureBits database dir/_something.bed
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