I'm using RSEM to simulate reads from previous experiments (
rsem-simulate-reads) - I have no problems getting the basics working, but having difficulties adjusting simulation based params.
Here's an example:
- Use RSEM to prepare reference (bowtie2 or STAR)
- Calculate expression
- Then simulate reads:
rsem-simulate-readswith something similar to this:
rsem-simulate-reads Human_ref/ref expression/results.stat/results.model \
expression/results.isoforms.results 0.1 500000 simulation/sim_data
The original data is PE, 150bp, non-stranded, bulk RNA-seq
From what I can gather, it is possible to adjust the model params (https://github.com/deweylab/RSEM/blob/master/model_file_description.txt) to simulate new reads with different library options. For example, say I wanted 50bp PE reads, or 50bp SE stranded reads.
Is this possible using RSEM? I know this is possible using Polyester (https://bioconductor.org/packages/release/bioc/vignettes/polyester/inst/doc/polyester.html), which I'm using, but was hoping to use RSEM as well.