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.