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.

needle-estimate 1.0.3                              2024-11-07                                 NEEDLE-ESTIMATE(1)