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  • Zimbobo
    Member
    • Mar 2010
    • 25

    RNA-Seq simulation

    Hello,

    does anyone know of any software that produces simulated RNA-Seq data. I am interested in questions like how many reads are needed for a good assembly with velvet for example, what read errors produce which problems in the assembly. Thanks in advance for any pointers.
  • krobison
    Senior Member
    • Nov 2007
    • 734

    #2
    You are probably better off downloading an RNA-Seq dataset from the Short Read Archive -- this is more likely to represent the real biases you will find in RNA-Seq data (such as strand, 3' vs 5', etc)

    Comment

    • brentp
      Member
      • Apr 2010
      • 72

      #3
      you could check out FluxSimulator.

      Comment

      • krobison
        Senior Member
        • Nov 2007
        • 734

        #4
        The FluxSimulator looks interesting, but someone needs to fix the pages -- there is a consistent typo which makes it impossible to read them aloud in polite company!

        Comment

        • vinay052003
          Member
          • Jan 2010
          • 59

          #5
          These are no doubt good suggestions. One simple way would be to take the mRNA sequences from the public database and chop them up randomly (in-silico). Repeat this process couple of times untill you don't get the desired coverage.

          Comment

          • lexa
            Member
            • Jun 2010
            • 17

            #6
            you can use dwgsim from the dnaa package. you can give read number, read length (even for paired-end data) and a reference.

            maq contains also a simulation tool which seems similar to dwgsim.

            Comment

            • micha
              Junior Member
              • Jan 2009
              • 1

              #7
              The FluxSimulator looks interesting, but someone needs to fix the pages -- there is a consistent typo which makes it impossible to read them aloud in polite company!
              Keith,
              someone fixed the page, I think you can read it aloud now the timestamp of the former html file read 00:58, was probably not the best moment of that day. Thanks for bringing this typo to attention!

              Comment

              • seqmagician
                Junior Member
                • Aug 2010
                • 3

                #8
                Link to FLuxSimulator paper.

                Could any one please point to me the link to FluxSimulator paper? I do find out in their web pages. Thanks.

                Comment

                • lexa
                  Member
                  • Jun 2010
                  • 17

                  #9
                  as far as I know, there is no paper about FluxSimulator.

                  Comment

                  • catbus
                    Member
                    • Feb 2011
                    • 21

                    #10
                    USeq: RNA-Seq Simulator (requires *real* data as input, however)

                    There's also "RNA Seq Simulator," which is part of USeq---note that this requires REAL RNA-seq data as an input, and then it simulates various types of factors that cause differential gene expression.

                    Comment

                    • greggrant
                      Member
                      • Dec 2008
                      • 28

                      #11
                      Originally posted by Zimbobo View Post
                      Hello,

                      does anyone know of any software that produces simulated RNA-Seq data. I am interested in questions like how many reads are needed for a good assembly with velvet for example, what read errors produce which problems in the assembly. Thanks in advance for any pointers.
                      Please try our simulator BEERS:

                      Comment

                      • jingjinghao
                        Junior Member
                        • Oct 2012
                        • 3

                        #12
                        Originally posted by greggrant View Post
                        Please try our simulator BEERS:

                        http://cbil.upenn.edu/BEERS/
                        Hi,sir, I have tried BEERS. Thank you for your good simulator. It did me a big favor.
                        Some questions:
                        (1)BEERS generates reads like: genes from combined gene models(RefSeq, AceView...)-->transcripts-->add polymorphisms-->reads-->add sequence error and position bias. Is it right?
                        (2)How does BEERS decide which and how many gene and transcript to be "expressed"?
                        (3)Reads are generated from transcripts according to which distribution?

                        Thank you very much!
                        Last edited by jingjinghao; 10-16-2012, 07:02 AM. Reason: misspelling

                        Comment

                        • Jegar
                          Junior Member
                          • Aug 2014
                          • 6

                          #13
                          There seems to be a broad range of RNA-Seq simulators. Has anyone done a comparison, or know of a paper that examines them empirically? I'd just be interested to know how their different features compare. The list I have compiled is this so far (apologies for doubles), some of these may be only for DNA-Seq simulation.

                          http://www.biomedcentral.com/1471-2164/13/74 - GemSim

                          http://bioinformatics.oxfordjournals...rmatics.btr708 - ART

                          https://github.com/jstjohn/SimSeq - SimSeq

                          https://popmodels.cancercontrol.canc...lux-simulator/ -FLUX Simulator

                          https://github.com/lh3/wgsim - wgsim in SAMtools

                          http://omictools.com/simulators2/ - Massive range of DNA-seq simulators

                          http://useq.sourceforge.net/cmdLnMen...NASeqSimulator RNAseq simulator

                          http://cbil.upenn.edu/BEERS/ BEERS


                          Importantly, is it better to use one of these simulators than to just download something from a Short Read archive? In which contexts?

                          Comment

                          • dpryan
                            Devon Ryan
                            • Jul 2011
                            • 3478

                            #14
                            I imagine such a paper would be difficult to get published (I can already see the reviewer comments of "not novel" and "too trivial", even though such a paper would end up being useful for the community).

                            Regarding when you might use a simulator vs. an actual experiment, the only benefit to a simulator is that you can know exactly where the reads should align and where their mismatches are. If you need to test the accuracy of an aligner, then that's something you need. Similarly, if you want to test methods for calling SNPs or finding RNA editing sites, then you need a dataset with known changes. Of course the error profiles of the resulting reads are never perfect, so you end up needing to use a real dataset too, just to compare raw alignment/call rates (you obviously can't know accuracy from that).

                            Comment

                            • Jegar
                              Junior Member
                              • Aug 2014
                              • 6

                              #15
                              Thanks for your reply and helpful clarification.

                              It sounds like a comparison of simulators might be good for a blog post - shame that a helpful piece of work like that wouldn't get published (I have to agree it would not be considered novel, despite there being no existing published comparison paper).

                              I am exploring error signatures produced through biological processes in the sequencing workflow, and am attempting to reproduce the workflow in silica. From what I gather, Flux Simulator might have some love for me but if not I'll get Python to do the heavy lifting.

                              Comment

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