NEEDLE-COUNT

NAME

needle-count - Get expression value depending on minimizers. This function is only used to test the validity of Needle’s estimation approach. It estimates the expression value for all sequences in the genome file based on the exact minimiser occurrences of the given sequence files.

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.

-g, --genome (std::filesystem::path)

Please provide one sequence file with transcripts. Default: "".

--exclude (std::filesystem::path)

Please provide one sequence file with minimizers to ignore. Default: "".

-p, --paired

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

VERSION

Last update:
needle-count version:
SeqAn version: 3.2.0