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https://github.com/chrisarg/bio-seqalignment-applications-sequencingsimulators-rnaseq-polyester

Enhancement the RNA simulator polyester to include polyA tails in the simulated sequences
https://github.com/chrisarg/bio-seqalignment-applications-sequencingsimulators-rnaseq-polyester

bioinformatics bioinformatics-tool rnaseq sequence simulator

Last synced: 19 days ago
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Enhancement the RNA simulator polyester to include polyA tails in the simulated sequences

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README 

        
NAME

    polyester_polyA.pl - A Perl application for enhancing the polyester RNA

    sequencing simulation tool.



VERSION

    version 0.02



SYNOPSIS

    polyester_polyA.pl [options]



DESCRIPTION

    The purpose of the application is to enhance the polyester RNA

    sequencing simulation tool by including polyA tails in the reference RNA

    being used to generate the simulated sequencing data. The application is

    a wrapper around the R package polyester, which only accounts for the

    processes of fragmentation, reverse complementation and sequencing when

    generating data. Note that the Perl application does not (at this

    moment) include the possibility of passing logspline R objects as

    parameters to the R script and the the polyester "simulate_experiment"

    function. The command line options are the same as the ones in the

    polyester R package, with the exception of: * The addition of the

    --taildist option, which is mandatory and specifies the tail

    distribution to be used. * The addition of the --distparams option,

    which is mandatory and specifies the parameters of the distribution. *

    The addition of the --maxseqs option, which is optional and specifies

    whether to break the single fasta file generated by the application into

    multiple files of a specified maximum number of sequences. * The

    addition of the --modformat option, which is optional and specifies the

    format for storing modifications (one of JSON, YAML, or MessagePack). *

    BONUS: provide a R script that can be used to control the polyester

    simulation process from the command line (polyester.R) All other

    parameters have the same interpretation and semantics as in the

    polyester R package.



OPTIONS

    --bias, -b [STRING]

        Fragment selection bias (optional).



    --distparams, -P [FLOAT1 FLOAT2 ...]

        Distribution parameters (mandatory, list of numeric values).



    --errormodel, -e [STRING]

        Error model (optional).



    --errorrate, -E [FLOAT]

        Error probability (optional).



    --fastafile, -f [PATH]

        Fasta file path (mandatory).



    --fcfile, -c [PATH]

        Fold change file path (optional).



    --fraglen, -F [INTEGER]

        Fragment length (average) (optional).



    --fragsd, -S [INTEGER]

        Fragment length (standard deviation) (optional).



    --gcbias, -g [INTEGER]

        GC bias (optional).



    --modformat, -m [INTEGER]

        Case insensitive format for storing modifications (one of JSON,

        YAML, or MessagePack) (optional).



    --maxseqs, -m [INTEGER]

        Maximum sequences per file (optional).



    --numreps, -n [INTEGER1 INTEGER2 ...]

        Number of replicates in each group (optional, list).



    --outdir, -o [PATH]

        Path to output directory (optional).



    --paired, -p [TRUE|FALSE]

        Paired reads (optional).



    --readlen, -R [INTEGER]

        Read length (optional).



    --readsfile, -r [PATH]

        Reads per transcript file path (optional).



    --seed, -d [INTEGER]

        Random seed (optional).



    --strandspec, -s [TRUE|FALSE]

        Strand specificity (optional).



    --taildist, -t [STRING]

        Tail distribution (mandatory).



    --writeinfo, -w [INTEGER]

        Save simulation info (optional).



EXAMPLES

      polyester_polyA.pl --fastafile myseq.fasta --taildist gamma \

      --distparams 125.0 1.0 0.0 250.0 --fraglen 100 --fragsd 10 \

      --numreps 1 --strandspec TRUE --readlen 75 --paired F \

      --maxseqs 1000 --modformat YAML --outdir /path/to/output



TODO

    *   Add the possibility of passing logspline R objects as parameters to

        the R script and the polyester "simulate_experiment" function.



    *   Add the possibility of adding UMI tags to sequences.



    *   Add the possibility of adding sequencing adapters to sequences.



SEE ALSO

    *   polyester 



        Polyester is an R package designed to simulate RNA sequencing

        experiments with differential transcript expression.Given a set of

        annotated transcripts, Polyester will simulate the steps of an

        RNA-seq experiment (fragmentation, reverse-complementing, and

        sequencing) and produce files containing simulated RNA-seq reads.

        Simulated reads can be analyzed using your choice of downstream

        analysis tools. Polyester has a built-in wrapper function to

        simulate a case/control experiment with differential transcript

        expression and biological replicates. Users are able to set the

        levels of differential expression at transcripts of their choosing.

        This means they know which transcripts are differentially expressed

        in the simulated dataset, so accuracy of statistical methods for

        differential expression detection can be analyzed.



        Polyester offers several unique features:



        * Built-in functionality to simulate differential expression at the

        transcript level * Ability to explicitly set differential expression

        signal strength * Simulation of small datasets, since large RNA-seq

        datasets can require lots of time and computing resources to analyze

        * Generation of raw RNA-seq reads, as opposed to alignments or

        transcript-level abundance estimates * Transparency/open-source code



AUTHOR

    Christos Argyropoulos 



COPYRIGHT AND LICENSE

    This software is copyright (c) 2024 by Christos Argyropoulos.



    This is free software; you can redistribute it and/or modify it under

    the same terms as the Perl 5 programming language system itself.