what do the genomic intervals in the results mean? about sierra HOT 1 CLOSED

The coordinates that are reported are the coordinates of the peaks. In some cases, they will overlap splice junctions, but the coordinates do not directly refer to specific splice junctions.

I've made an update to the code so that peaks overlapping splice junctions are better recorded and can be displayed in the output of DUTest. If you want to go deeper, the peak output file contains a column 'exon.pos' that contains the coordinates of the exons in the peaks that span splice junctions.

You'll need to re-run the pipeline from peak calling to take advantage of the junction annotations. When running DUTest, set include.annotations = TRUE and your output will include a column indicating whether a peak is 'across-junctions' or not ('no-junctions').

Hope that's helpful.

from sierra.