.TH NEEDLE-COUNT 1 "" "needle-count " ""
.SH 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.
.SH POSITIONAL ARGUMENTS
.TP
\fBARGUMENT-1\fP (\fIList\fP of \fIstd::filesystem::path\fP)
Please provide at least one sequence file. Default: []. 
.SH OPTIONS
.SS Basic options:
.TP
\fB-h\fP, \fB--help\fP
Prints the help page.
.TP
\fB-hh\fP, \fB--advanced-help\fP
Prints the help page including advanced options.
.TP
\fB--version\fP
Prints the version information.
.TP
\fB--copyright\fP
Prints the copyright/license information.
.TP
\fB--export-help\fP (std::string)
Export the help page information. Value must be one of [html, man].
.TP
\fB-k\fP, \fB--kmer\fP (\fIunsigned 8 bit integer\fP)
Define k-mer size for the minimisers. Default: 20. Default: 20. 
.TP
\fB-w\fP, \fB--window\fP (\fIunsigned 32 bit integer\fP)
Define window size for the minimisers. Default: 60. Default: 0. 
.TP
\fB--shape\fP (\fIunsigned 64 bit integer\fP)
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. 
.TP
\fB--seed\fP (\fIunsigned 64 bit integer\fP)
Define seed for the minimisers. Default: 0. 
.TP
\fB-o\fP, \fB--out\fP (\fIstd::filesystem::path\fP)
Directory, where output files should be saved. Default: "./". 
.TP
\fB-t\fP, \fB--threads\fP (\fIunsigned 8 bit integer\fP)
Number of threads to use. Default: 1. Default: 1. 
.TP
\fB--include\fP (\fIstd::filesystem::path\fP)
Please provide one sequence file with transcripts. 
.TP
\fB--genome\fP (\fIstd::filesystem::path\fP)
Please provide one *.genome file created with the genome command. Default: "". 
.TP
\fB-p\fP, \fB--paired\fP
If set, experiments are paired. Default: Not paired.
.SH VERSION
\fBLast update: \fR
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\fBneedle-count version: \fR
.br
\fBSeqAn version: \fR3.3.0