[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	16738167
Known Splicing Events:	16559710
Partial Novel Splicing Events:	80571
Novel Splicing Events:	84182
Filtered Splicing Events:	13704

Total splicing  Junctions:	104927
Known Splicing Junctions:	97339
Partial Novel Splicing Junctions:	2519
Novel Splicing Junctions:	5069

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Create BED file ...
Create Interact file ...