NAME

    count_tags_per_genic_element.pl

SYNOPSIS

    count_tags_per_genic_element.pl [options/parameters]
    

DESCRIPTION

    Measures the read count for each genic element (ie. transcript, gene, exon, intron)"
    *Transcript count is measured only for its exons."
    *Gene count is measured only for its exonic regions."

OPTIONS AND ARGUMENTS

    Input
      Database options (DBIC)
        -driver <Str>        specify driver for database. This can be mysql, SQLite, etc.
        -database <Str>      database name.
        -table <Str>         database table with data.
        -host <Str>          hostname for database connection.
        -user <Str>          username for database connection.
        -password <Str>      password for database connection.
      Gene Models
        -gtf <Str>           GTF file for transcripts.
        -transcript_to_gene_file <Str>   a file that maps gene names to transcript ids.
    
    Output
        -ofile_prefix <Str>  prefix for the path used to create output files - path will be created.
    
    Input Filters.
        -min_length <Int>    reads with smaller length than this value are excluded.
        -max_length <Int>    reads with larger length than this value are excluded.
        -no_repeat           keep only non-repeat mapping reads.
        -with_deletion       keep only reads with deletions (HITS-CLIP).
        -with_TC             keep only reads with T -> C mismatch (PAR-CLIP).
    
    Other options.
        -v                 verbosity. If used progress lines are printed.
        -h                 print this help;