Exon-exon junctions: compare experimental transcripts to reference annotation
You can use the script that comes with minimap2:

# install the k8 javascript shell
curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
cp k8-0.2.4/k8-`uname -s` $HOME/bin/k8    # assuming $HOME/bin in your $PATH

# acquire the latest minimap2
git clone https://github.com/lh3/minimap2.git

# print novel/erroneous junctions
minimap2/misc/paftools.js junceval -e anno.gtf rna-seq.sam &gt; output.txt


Some example output:

P       read1    4       chr2    227332588       227340301       [(227332588,227340291)]
P       read2    1       chr9    19376379        19376489        [(19376388,19376493)]
P       read2    3       chr9    19378506        19378707        [(19378514,19378707)]
N       read3    1       chr1    160647335       160647472
N       read3    2       chr1    160647581       160659672


Here column 4–6 gives junctions not in the annotation. Column 7, if not empty, gives the list of annotated junctions/introns that overlap the junction in read alignment. Note that a big fraction of outputted records are errors in read alignment.