Usually for DNA we map PE data to the genome and then use picard's CollectInsertSizeMetrics to give a insert size distribution. For RNA PE data we map to the genome with STAR and then want to look at insert size. I don't think that CollectInsertSizeMetrics will work, since it will think that spliced reads actually have the entire intron as the insert, thus artificially increasing the insert size. Is there a splicing aware tool that will calculate the actual insert size after mapping to the genome? I realize I can also map to the transcriptome and CollectInsertSizeMetrics should work, but I'm wondering if there is an alternate to having to do both mappings.