Man page - needle-estimate(1)

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Manual

NEEDLE-ESTIMATE

NAME
POSITIONAL ARGUMENTS
OPTIONS
Basic options:
VERSION
URL
LEGAL

NAME

needle-estimate - Estimate expression value of transcript based on the Needle index.

POSITIONAL ARGUMENTS

ARGUMENT-1 ( std::filesystem::path )

Please provide a sequence file.

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].

-i , --in ( std::filesystem::path )

Directory where input files can be found. Default: "./".

-o , --out ( std::filesystem::path )

Directory, where output files should be saved. Default: "expressions.out".

-t , --threads ( unsigned 8 bit integer )

Number of threads to use. Default: 1. Default: 1.

-m , --normalization-mode

Set, if normalization is wanted. Normalization is achieved bydividing the expression value with the expression threshold of the first ibf. Only make sense if every bin has its own expression thresholds (which is the case if expression thresholds were generated automatically).Default: False.

VERSION

Last update: 2024-11-07
needle-estimate version: 1.0.3
SeqAn version: 3.3.0

URL

https://github.com/seqan/needle

LEGAL

needle-estimate Copyright: BSD 3-Clause License
Author: Mitra Darvish
SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
In your academic works please cite: 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 .