Closed lutfia95 closed 2 years ago
Thank you for your using PBSIM2. If you know --difference-ratio you want to specify for each accuracy, you should specify those values. If not, I recommend specifying the same value (such as 23:31:46 for Nanopore) for all accuracies.
Thank you for your answer, so if I set --difference-ratio 0:0:0
then I am simulating error free reads.
Is it enough to set the --accuracy-mean
or should I also set the --accuracy-min
and --accuracy-max
?
E.g. I wan to simulate reads with error rate 1%, so I set the --accuracy-mean 0.99
and also --accuracy-min 0.99
and --accuracy-max 0.99
?
What are this values mean? so e.g. 23:31:46 ((substitution:insertion:deletion)). Is that mean, that I have then 23 substitutions pro read? or what is exactly the meaning of the values?
best, Ahmad
Is it enough to set the --accuracy-mean or should I also set the --accuracy-min and --accuracy-max? E.g. I wan to simulate reads with error rate 1%, so I set the --accuracy-mean 0.99 and also --accuracy-min 0.99 and --accuracy-max 0.99 ?
PBSIM2 stochastically simulates reads, so it cannot simulate reads exactly with the specified accuracy (except error-free), and the accuracy of the generated reads follows an exponential distribution. Also, PBSIM2 is designed to simulate error-prone reads, so it cannot generate data with an average accuracy of 99%. About 96% should be the limit.
What are this values mean? so e.g. 23:31:46 ((substitution:insertion:deletion)). Is that mean, that I have then 23 substitutions pro read? or what is exactly the meaning of the values?
--difference-ratio specifies the ratio of error types introduced to the read. For example, if you specify 1: 2: 3, the ratio of the number of substitution, insertion, and deletion will be approximately 1: 2: 3. Specifying 2: 4: 6 or 10:20:30 are equal to 1: 2: 3.
Thank you for the answers!
Hi,
I am not sure, how can I use the option
--difference-ratio
correctly with different mutations.E.g.
pbsim genom_.fasta --length-min 360 --length-max 500 --accuracy-min 1.00 --acuracy-mean 1.00 --hmm_model R94.model --difference-ratio 0:0:0
gives 100% accuracy.If I want to try e.g. mean accuracy 99%, 95% or even 85%. How should I change the
--difference-ratio
according to accuracy changes?Best, Ahmad