Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Announcing rlsim, a package for simulating RNA-seq library preparation

    What is the rlsim package?

    The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection. It allows for a systematic exploration of the effects of the individual biasing factors and their interactions on downstream applications by simulating data under a variety of parameter sets.

    The implicit simulation model implemented in the main tool (rlsim) is inspired by actual library preparation protocols and it is more general than the models used by the bias correction methods hence it allows for a fair assessment of their performance.

    Although the simulation model was kept as simple as possible in order to aid usability, it still has too many parameters to be inferred from data produced by standard RNA-seq experiments. However, simulating datasets with properties similar to specific datasets is often useful. To address this, the package provides a tool (effest) implementing simple approaches for estimating the parameters which can be recovered from standard RNA-seq data (GC-dependent amplification efficiencies, fragment size distribution, relative expression levels).

    The latest release and the package source is available from the rlsim GitHub repository: https://github.com/sbotond/rlsim

    Citing the rlsim package

    An associated manuscript is in preparation, meanwhile the package should be cited as:

    Botond Sipos, Tim Massingham and Nick Goldman (2013): rlsim - a package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-doc.

    Getting more help

    Please consult the package documentation for more help on the tools and the technical background.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
37 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
47 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X