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NAME

TraFic_cluster.pl - Generate files suitable for input to cluster discovery

SYNOPSIS

TraFic_cluster.pl [-h] -o /some/path/ -r %.out -f %.fa

  Required options:

    --rm      (-r)  Repeat masker *.out files
    --fa      (-f)  Modified fasta format originally supplied to repeat masker

      NOTE: Both can be defined once with/without wildcard % or multiple times

  Other options:

    --output  (-o)  Output written to specified folder (current working directory otherwise):
                      - pos_hits.txt
                      - neg_hits.txt
                      - pos_clusters.txt
                      - neg_clusters.txt

    --min     (-m)  Minimum number of reads required to emit a cluster. [5]
    --paired  (-p)  Excludes single end mapped Alu from clustering

    --help    (-h)  This message

  Examples:
    TraFic_cluster.pl -o $HOME/trafic -r COLO-829.%.fa.out -f COLO-829.fa

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