NAME

       needle-count  -  Get  expression  value  depending  on  minimizers.  This  function  is an
       alternative to pseudoaligners like kallisto. It estimates the  expression  value  for  all
       sequences  in  the  genome  file  based  on  the  exact minimiser occurrences of the given
       sequence files. Please run genome beforehand to create the genome file.

POSITIONAL ARGUMENTS

       ARGUMENT-1 (List of std::filesystem::path)
              Please provide at least one sequence file. Default: [].

OPTIONS

   Basic options:
       -h, --help
              Prints the help page.

       -hh, --advanced-help
              Prints the help page including advanced options.

       --version
              Prints the version information.

       --copyright
              Prints the copyright/license information.

       --export-help (std::string)
              Export the help page information. Value must be one of [html, man].

       -k, --kmer (unsigned 8 bit integer)
              Define k-mer size for the minimisers. Default: 20. Default: 20.

       -w, --window (unsigned 32 bit integer)
              Define window size for the minimisers. Default: 60. Default: 0.

       --shape (unsigned 64 bit integer)
              Define a shape for the minimisers by the decimal of a bitvector, where 0 symbolizes
              a position to be ignored, 1 a position considered. Default: ungapped. Default: 0.

       --seed (unsigned 64 bit integer)
              Define seed for the minimisers. Default: 0.

       -o, --out (std::filesystem::path)
              Directory, where output files should be saved. Default: "./".

       -t, --threads (unsigned 8 bit integer)
              Number of threads to use. Default: 1. Default: 1.

       --include (std::filesystem::path)
              Please provide one sequence file with transcripts.

       --genome (std::filesystem::path)
              Please provide one *.genome file created with the genome command. Default: "".

       -p, --paired
              If set, experiments are paired. Default: Not paired.

VERSION

       Last update:
       needle-count version:
       SeqAn version: 3.3.0