In reviewing the code repository for this paper I was unable to find the program arguments used to analyze the results.

What options to Blast+, TransDecoder, and BLAT were used?

Where are the R scripts that made the figures?

Thanks,

I was not able to find it at the given URL.

The newest version of GRCm37 I could find was from Ensembl build 67 at (ftp://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz)

The par.sim file references a "Mus.gtf" so I am unable to verify what version you actually used.

Although AllPathsLG and SGA did not report the number of corrected reads (annoyingly, I agree), it is rather straighforward to determine this yourself with a simple script, especially as the output files probably maintain the same order? I am amazed at the wide range in correction rates.