I performed a splicing analysis using hisat2 as a mapper, everything goes perfect, as expected. But, by using STAR I am not able to find any splicing event (splice junctions). I am using default parameters in both cases and obviously the same data. I am very familiar using hisat2 but no using STAR, my question is somebody is familiar with STAR to do this class of analysis? Am I missing something? It is quite surprising to me since STAR this is specially designed for spliced transcripts.
I check splicing reads in star`s bam by using (they actually exist, although not in the same proportion than in hisat2's results):
samtools view my.bam | awk '($6 ~ /N/)'
But I can not visualize the junctions track on IGV.