Category
Generic
Usage
chainNet in.chain target.sizes query.sizes target.net query.net
Manual
This tool is part of UCSC Genome Browser's utilities.
where:
in.chain is the chain file sorted by score
target.sizes contains the size of the target sequences
query.sizes contains the size of the query sequences
target.net is the output over the target genome
query.net is the output over the query genome
options:
-minSpace=N - minimum gap size to fill, default 25
-minFill=N - default half of minSpace
-minScore=N - minimum chain score to consider, default 2000.0
-verbose=N - Alter verbosity (default 1)
-inclHap - include query sequences name in the form *_hap*. Normally
these are excluded from nets as being haplotype
pseudochromosomes
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