hgWiggle

Reference Code backup Executable files

Fetch wiggle data from UCSC Genome Browser's database or a wig file

Category

Fetch Data

Usage

hgWiggle [options] <track names ...>

Manual

This tool is part of UCSC Genome Browser's utilities.

If you want to extract signals from a bigWig file, consider using bigWigToBedGraph or bigWigToWig.

Options

  • -db=<database>: use specified database
  • -chr=chrN: examine data only on chrN
  • -chrom=chrN: same as -chr option above
  • -position=[chrN:]start-end: examine data in window start-end (1-relative). Note: the chrN: is optional)
  • -chromLst=<file>: file with list of chroms to examine
  • -doAscii: perform the default ascii output, in addition to other outputs
    • Any of the other -do outputs (-doStats, -doBed) turn off the default ascii output
    • WARNING this ascii output is 0-relative offset which is not the normal wiggle input format. Use the -lift argument -lift=1 to get 1-relative offset
  • -lift=<D>: lift ascii output positions by D (0 default)
  • -rawDataOut: output just the data values, nothing else
  • -htmlOut: output stats or histogram in HTML instead of plain text
  • -doStats: perform stats measurement, default output text, see -htmlOut
  • -doBed: output bed format
  • -bedFile=<file>: constrain output to ranges specified in bed
  • -dataConstraint='DC': where DC is one of < = >= <= == != 'in range'
  • -ll=<F>: lowerLimit compare data values to F (float) (all but 'in range')
  • -ul=<F>: upperLimit compare data values to F (float) (need both ll and ul when 'in range')
  • -help: display more examples and extra options (to stderr)


When no database is specified, track names will refer to .wig files

Examples

In the following examples, we are going to extract GC percent data (5bp resolution) of chromosome I for Stickleback reference genome release gasAcu1.

With local file

Use hgWiggle to extract signals from a local wig file requires not only the wig file but also a wib file (binary files which are interpreted by the data found in the .wig files.)

# first get the files
$ rsync -aP rsync://hgdownload.soe.ucsc.edu/goldenPath/gasAcu1/database/gc5Base.txt.gz .
$ gunzip gc5Base.txt.gz
$ ln -s gc5Base.txt gc5Base.wig
$ rsync -aP rsync://hgdownload.soe.ucsc.edu/gbdb/gasAcu1/wib/gc5Base.wib .

Then call hgWiggle:

$ hgWiggle -chr=chrI gc5Base > chrI.wig
With UCSC's database
$ hgWiggle -db=gasAcu1 -chr=chrI gc5Base > chrI.wig

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