hgGcPercent [options] database nibDir


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

nibDir can be a .2bit file, a directory that contains a
database.2bit file, or a directory that contains *.nib files.
Loads gcPercent table with counts from sequence.
-win= - change windows size (default 20000)
-noLoad - do not load mysql table - create bed file
-file= - output to (stdout OK) (implies -noLoad)
-chr= - process only chrN from the nibDir
-noRandom - ignore randome chromosomes from the nibDir
-noDots - do not display ... progress during processing
-doGaps - process gaps correctly (default: gaps are not counted as GC)
-wigOut - output wiggle ascii data ready to pipe to wigEncode
-overlap=N - overlap windows by N bases (default 0)
-verbose=N - display details to stderr during processing
-bedRegionIn=input.bedRead in a bed file for GC content in specific regions and write to bedRegionsOut
-bedRegionOut=output.bed Write a bed file of GC content in specific regions from bedRegionIn

calculate GC percent in 5 base windows using a 2bit assembly (dp2):
hgGcPercent -wigOut -doGaps -win=5 -file=stdout -verbose=0 \
dp2 /cluster/data/dp2 \
| wigEncode stdin gc5Base.wig gc5Base.wib

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