Introduce errors in reference transcripts according to external dataset error model I would like to modify some reference transcripts from Ensembl (D. melanogaster) to introduce a controlled rate of random errors in the sequences. The idea would be to introduce random base substitutions in these sequences, no indels for now, because I would like to keep the transcript sequence length as it is in the reference. 

The rate of error per transcript will be determined according to an error profile computed from an external set of RNA-seq reads (e.g., generated with ONT MinION)

The aim of this modification would be to establish a rough benchmark of the performances of aligners to use over transcripts from spliced reads (rna-to-genome), aka with more than one exon.

Any idea of which software would be best for this purpose?
Do any of the answers for this question help? Karel Brinda has mentioned a few read simulators in the answer to that question, and has a thesis with more information.

Excluding INDEL errors doesn't sound like a good idea; length can still be preserved even if doing that, it just needs an adjustment at the end of the sequence. Note that if you're trying to model nanopore reads, what you're really modelling is the base-caller, rather than the sequencer. I mention this in more detail in my answer.

In most cases where errors are modelled, I find it better to use publicly-available data instead. Especially for nanopore data, there are unmodelled systematic errors in the base-callers and sequencer that can't be simulated using any programs (because they are unmodelled). The following paper would be a good place to start for cDNA sequences, which looks at single-cell data from mouse (C57Bl/6) B1a cells:

http://www.biorxiv.org/content/early/2017/04/13/126847

Illumina and ONT reads for that study can be found in SRA under accession number SRP082530.

I don't know of any recent D. melanogaster studies that have been done using nanopore. There's always the option of spending $1000 on a purchase of a MinION with an RNA starter kit to do the study yourself. Here's an older targeted gene study, but bear in mind that it was using an R7.3 flow cell, so errors rates will be much higher than what is currently available:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0777-z