Category
Multiple sequence alignments / Conservation
Usage
mafFrags database track in.bed out.maf
Manual
This tool is part of UCSC Genome Browser's utilities.
options:
-orgs=org.txt - File with list of databases/organisms in order
-bed12 - If set, in.bed is a bed 12 file, including exons
-thickOnly - Only extract subset between thickStart/thickEnd
-meFirst - Put native sequence first in maf
-txStarts - Add MAF txstart region definitions ('r' lines) using BED name
and output actual reference genome coordinates in MAF.
-refCoords - output actual reference genome coordinates in MAF.
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