PSLMAP(1)

NAME
pslMap.pl combine two psl files transitively

SYNOPSIS
pslMap.pl [ --filterunspliced ] --in=in.psl --map=map.psl --out=out.psl

    If in and map are considered to be mappings from the query to the target, then
    out is the consecutive application of in and map. The map is assumed to not contain mismatches.
    In contrast to the UCSC pslMap C program, this program is reporting the mismatches of in.psl in
    the output alignments.

OPTIONS
  in               psl input file, e.g. from an alignment of transcript reads against mRNA sequences
  map              psl input file, e.g. from an alignment of mRNA sequences against a genome
                   The queries of map must be the targets of in.
  out              psl output file, e.g. the inferred alignment of transcript reads against the genome
  filterunspliced  alignments in in.psl that do not cover an intron in map.psl are not reported in out.psl
  minmatch         filter out alignments with a number of matches (first column) that is below this (default: 0)

DESCRIPTION
    The planned typical usage of this script is for RNA-Seq alignment.
    Then in.psl can contain alignments of reads against small exon-exon windows (or candidates thereof)
    and can be done with a fast almost exact mapper that does no spliced alignments.
    out.pl will then be the spliced alignments of the reads against the genome.
    The option --filterunspliced can then be used to ensure that read alignments are not reported twice.
    The unspliced alignments can be done directly to the genome and the spliced only through this indirect approach.
    Example input visualized:

        map target (genome)
     \           \      /           /
      \           \    /           /
       \           \  /           /
        \           \/           /
         ------------------------   map query = in target (mRNA)
           -- ----  -----   ---
          / / |  |  \   \   | |
         / /  |  |   \   \  | |
        / /   |  |    \   \ | |
       / /    |  |     \   \| |
       --     ----      -------
       in query (transcript reads)