Category
Generic
Usage
wigEncode [options] wigInput wigFile wibFile
Manual
This tool is part of UCSC Genome Browser's utilities.
wigInput - wiggle ascii data input file (stdin OK)
wigFile - .wig output file to be used with hgLoadWiggle
wibFile - .wib output file to be symlinked into /gbdb/
/wib/
This processes the three data input format types described at:
http://genome.ucsc.edu/encode/submission.html#WIG
(track and browser lines are tolerated, i.e. ignored)
options:
-lift= - lift all input coordinates by D amount, default 0
- can be negative as well as positive
-allowOverlap - allow overlapping data, default: overlap not allowed
- only effective for fixedStep and if fixedStep declarations
- are in order by chromName,chromStart
-noOverlapSpanData - check for overlapping span data
-wibSizeLimit= - ignore rest of input when wib size is >= N
Example:
hgGcPercent -wigOut -doGaps -file=stdout -win=5 xenTro1 \
/cluster/data/xenTro1 | wigEncode stdin gc5Base.wig gc5Base.wib
load the resulting .wig file with hgLoadWiggle:
hgLoadWiggle -pathPrefix=/gbdb/xenTro1/wib xenTro1 gc5Base gc5Base.wig
ln -s `pwd`/gc5Base.wib /gbdb/xenTro1/wib
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