I would like to get help to find tools that generated realistic rna-seq reads. Does anybody know such tools?
I need these tools to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Currently, I am using a function that generates simulating data that simulates reads from a given reference isoforms. First, it sub-samples the isoforms (represents biological sample), then samples the reads from this sub-sampled data.
An example tool is something like Polyester (https://academic.oup.com/bioinformatics/article/31/17/2778/183245), but this paper was published in 2015. I see another one add signal to RNA-seq datasets to make it more realistic (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3450-9).
If there are new (popular) tools to generate realistic rna-seq reads, it would be helpful to the experiment that I am trying to work on!
There is plenty of real data now available in repositories. Perhaps that is the reason there are no tools written to simulate data of late. You can search SRA to look for datasets that fit your needs. You may need to read papers that describe isoform level analyses and then find the datasets in public repositories.