needle-count - Get expression value depending on minimizers. This function is an alternative to

needle-countCopyright: BSD 3-Clause License
       Author: Mitra Darvish
       SeqAnCopyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
       Inyouracademicworkspleasecite:  Needle: a fast and space-efficient prefilter for estimating the
       quantification of very large collections of expression experiments; Mitra Darvish, Enrico Seiler,  Svenja
       Mehringer,  René  Rahn,  and  Knut  Reinert; Bioinformatics, Volume 38, Issue 17, 1 September 2022, Pages
       4100-4108. doi: https://doi.org/10.1093/bioinformatics/btac492
       For full copyright and/or warranty information see --copyright.

needle-count 1.0.3                                 2024-11-07                                    NEEDLE-COUNT(1)

       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.

Basicoptions:-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 (unsigned8bitinteger)
              Define k-mer size for the minimisers. Default: 20. Default: 20.

       -w, --window (unsigned32bitinteger)
              Define window size for the minimisers. Default: 60. Default: 0.

       --shape (unsigned64bitinteger)
              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 (unsigned64bitinteger)
              Define seed for the minimisers. Default: 0.

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

       -t, --threads (unsigned8bitinteger)
              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.

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

       https://github.com/seqan/needle

Lastupdate: 2024-11-07
       needle-countversion: 1.0.3
       SeqAnversion: 3.3.0