Category
Generic
Usage
axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain
Manual
This tool is part of UCSC Genome Browser's utilities.
Where tNibDir/qNibDir are either directories full of nib files, or the
name of a .2bit file
options:
-psl Use psl instead of axt format for input
-faQ qNibDir is a fasta file with multiple sequences for query
-faT tNibDir is a fasta file with multiple sequences for target
-minScore=N Minimum score for chain, default 1000
-details=fileName Output some additional chain details
-scoreScheme=fileName Read the scoring matrix from a blastz-format file
-linearGap=
Specify type of linearGap to use.
*Must* specify this argument to one of these choices.
loose is chicken/human linear gap costs.
medium is mouse/human linear gap costs.
Or specify a piecewise linearGap tab delimited file.
sample linearGap file (loose)
tablesize 11
smallSize 111
position 1 2 3 11111 2111 121113211172111152111 252111
qGap 325 360 400 450 600 1100 3600 7600 156003160056600
tGap 325 360 400 450 600 1100 3600 7600 156003160056600
bothGap 625 660 700 750 900 1400 4000 8000 160003200057000
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