I'm wondering what to do in order to create a custom error model. I would like to create a simulation for 100 base pair reads.
Here, 4.5.3 - Output Read Sequences it says
With the values '35' or '76', default error models are provided for the corresponding read lengths, otherwise the path to a custom error model file is expected.
But, here 4.5.4 - Error Models it says
Since Version 1.0.3, the simulator model scaled to support read length not explicitly supported by the model. With this, you can for example use the 76bp error model and simulate error for 100bp reads
So do I need to generate a custom error model or not?
if yes, are there more detailed instructions about the procedure using GEM ? If not, would I just enter READ_LENGTH 100 and ERR_FILE 76 ?
no, you don't need to create a custom model. The default models will be scaled (so a little bit less accurate) but will work fine. I am still working on on update on the error model creation. The problem is that the current GEM format changed, so what we have in the Simulator currently only works with an old version of GEM. I will try to update the model creation and implement support for SAM/BAM files.
I would also greatly appreciate the possibility to have a custom error model generated from bam/sam files. It would make this tools much more usefull.
Corresponding request for improvement filed: