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App-SimulateReads-0.11
⭐ Starred 19 / App::SimulateReads::Command::Simulate::Transcriptome

NAME

App::SimulateReads::Command::Simulate::Transcriptome - simulate subcommand class. Simulate transcriptome sequencing

VERSION

version 0.11

SYNOPSIS

simulate_reads simulate transcriptome [options] -f <expression-matrix> <fasta-file>

Arguments:
 a fasta-file 

Mandatory options:
 -f, --weight-file        an expression-matrix file

Options:
 -h, --help               brief help message
 -M, --man                full documentation
 -v, --verbose            print log messages
 -p, --prefix             prefix output [default:"out"]	
 -o, --output-dir         output directory [default:"."]
 -j, --jobs               number of jobs [default:"1"; Integer]
 -z, --gzip               compress output file
 -n, --number-of-reads    set the number of reads
                          [default:"1000000", Integer]
 -t, --sequencing-type    single-end or paired-end reads
                          [default:"paired-end"]
 -q, --quality-profile    illumina sequencing system profiles
                          [default:"hiseq"]
 -e, --sequencing-error   sequencing error rate
                          [default:"0.005"; Number]
 -r, --read-size          the read size [default:"101"; Integer]
 -m, --fragment-mean      the fragment mean size for paired-end reads
                          [default:"300"; Integer]
 -d, --fragment-stdd      the fragment standard deviation size for
                          paired-end reads [default:"50"; Integer]

DESCRIPTION

Simulate transcriptome sequencing.

OPTIONS

--help

Print a brief help message and exits.

--man

Prints the manual page and exits.

--verbose

Prints log information to standard error

--prefix

Concatenates the prefix to the output-file name.

--output-dir

Creates output-file inside output-dir. If output-dir does not exist, it is created recursively

--jobs

Sets the number of child jobs to be created

--gzip

Compress the output-file with gzip algorithm. It is possible to pass --no-gzip if one wants uncompressed output-file

--read-size

Sets the read size. For now the unique valid value is 101

--number-of-reads

Sets the number of reads desired. This is the default option for transcriptome sequencing simulation

--sequencing-type

Sets the sequencing type to single-end or paired-end

--fragment-mean

If the sequencing-type is set to paired-end, it sets the fragment mean

--fragment-stdd

If the sequencing-type is set to paired-end, it sets the fragment standard deviation

--sequencing-error

Sets the sequencing error rate. Valid values are between zero and one

--quality-profile

Sets the illumina sequencing system profile for quality. For now, the unique valid values are hiseq and poisson

--weight-file

A valid weight file is an expression-matrix file with 2 columns. The first column is for the seqid and the second column is for the count. The counts will be treated as weights

AUTHOR

Thiago L. A. Miller <tmiller@mochsl.org.br>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2018 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007