Positive controls not detected (FRASER2)

[sli0001]

Hi,

Thank you for the useful pipeline!

I have been able to successfully run the Aberrant Splicing module (FRASER2) inside DROP on 85 STAR-aligned BAM files (paired, reverse strand), sequenced in the same conditions and from the same tissue type. When running DROP I supply a gene list, and the output results.tsv file contains ~630 events detected.

However, we have some positive controls that have not been detected. These are the positive control cases inside the results_gene_all.tsv file (I have redacted seqnames , start/end, hgncSymbol, etc.):

seqnames	start	end	width	strand	sampleID	hgncSymbol	type	pValue	padjust	psiValue	deltaPsi	counts	totalCounts	meanCounts	meanTotalCounts	nonsplitCounts	nonsplitProportion	nonsplitProportion_99quantile	annotatedJunction	pValueGene	padjustGene
-	-	-	625	+	-	-	jaccard	0.0040588	1	0.88	-0.09	2162	2453	3108.96	3156.67	63	0.03	0.09	both	0.016235	1   							
-	-	-	6780	-	-	-	jaccard	0.0077601	1	0.64	0.3	35	55	19.38	67.75	18	0.33	0.85	both	0.20952	1																								
-	-	-	374	+	-	-	jaccard	0.018634	1	0.32	-0.31	13	41	19.12	31	16	0.39	0.54	both	0.76398	1

Do you have any ideas on what caused these positive controls to have a p-adjust=1? Is increasing the sample size the only way to improve these results, or is there another or better way?

Thank you for the help,
Song