Category

Format Conversion


Usage

lavToAxt in.lav tNibDir qNibDir out.axt


Manual

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

tNibDir/qNibDir are either directories full of nib files, or a single twoBit file

Options

  • -fa qNibDir: is interpreted as a fasta file of multiple dna seq instead of directory of nibs
  • -tfa tNibDir: is interpreted as a fasta file of multiple dna seq instead of directory of nibs
  • -dropSelf: drops alignment blocks on the diagonal for self alignments
  • -scoreScheme=fileName: Read the scoring matrix from a blastz-format file. (only used in conjunction with -dropSelf, to rescore alignments when blocks are dropped)
     


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