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 (
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
The rlsim manuscript is now on arXiv, with the analysis pipeline at https://github.com/sbotond/paper-rlsim:
- Botond Sipos, Greg Slodkowicz, Tim Massingham, Nick Goldman (2013) Realistic simulations reveal extensive sample-specificity of RNA-seq biases arXiv:1308.3172
Getting more help
Please consult the package documentation for more help on the tools and the technical background.
Also feel free to ask questions on BioStar, I will monitor the