Wednesday, February 8, 2012

RNA-Seq Read Simulator

RNA-Seq is now a common protocol to study the expression of genes or transcripts. For research purposes, there are many simulators to simulate RNA-Seq reads, like Flux Simulator. But many times I found it hard to use because: 1) there are complicated parameters, 2) it requires large memory and 3) it crushes frequently. So I wrote a few scripts to generate simulated RNA-Seq reads, and publish them in a package "RNASeqReadSimulator".

 RNASeqReadSimulator is a set of scripts generating simulated RNA-Seq reads. It provides users a simple tool to generate RNA-Seq reads for research purposes, and a framework to allow experienced users to expand functions. RNASeqReadSimulator offers the following features:

  1. It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. 
  2. It is able to generate RNA-Seq reads that have a specified positional bias profile. 
  3. It is able to simulate random read errors from sequencing platforms. 
  4. The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions.
The webpage of RNASeqReadSimulator is here. You can find the source code in GitHub.


  1. Hey I tried using the tools But I faced some errors.
    I would be very thankful if you good help me sort out these errors at the earliest.
    I hereby provide you fresh outputs.

    Chr1 0 30427671 chromosome . .
    Chr1 3630 3759 five_prime_UTR . +
    Chr1 3630 3913 exon . +
    Chr1 3630 5899 gene . +
    Chr1 3630 5899 mRNA . +
    Chr1 3759 3913 CDS . +
    Chr1 3759 5630 protein . +
    Chr1 3995 4276 CDS . +
    Chr1 3995 4276 exon . +
    Chr1 4485 4605 CDS . +

    > -e -4,4 out.bed
    Mean and variance for lognormal distribution: -4.0,4.0
    #ID Length Dir Exons Position GroupID NIsoformInGroup Explv

    > --statonly TAIR10_GFF3_genes.sorted.BED
    #ID Length Dir Exons Position GroupID NIsoformInGroup

    > --stranded -n 100 -l 88 -o out.bed -f 12 --stranded TAIR10_GFF3_genes.bed

    Read count: 100
    Read length: 88
    Output bed file: out.bed
    Field: 12
    Assigning weights...
    Error: incorrect number of fields (should be 12)
    Error: incorrect number of fields (should be 12)
    Error: incorrect number of fields (should be 12)
    Error: incorrect number of fields (should be 12)
    Error: incorrect number of fields (should be 12)
    Error: incorrect number of fields (should be 12)
    Error: incorrect number of fields (should be 12)

    Total 590264 lines...
    Total 0 reads...

    What exactly is the error related to field I have changed the value of fields n number of times form 7 to 24 including 12 but everytime I get the same error
    And as for the generation of expression profile
    all I get it single line..nothing else.
    How exactly does this work.Could you clarify.
    Ganga Jeena

    1. Can this tools also generate fastq reads.
      If Bed files do not have quality information fastq can not be generated from bed file by bedtools.
      Ganga Jeena

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