TABLE 1.

Summary of the number genes and transcripts generated/retained at each step in the transcriptome reconstruction pipeline. The percent of total transcripts identified by each source at each step is shown in parenthesis. The rat Ensembl reference transcriptome (v.99) was used as input for StringTie, along with whole brain RNA sequencing data, to characterize alternative splicing in brain of the HXB/BXH recombinant inbred rat panel. RNA sequencing data was likewise used, in conjunction with DNA sequence of the rat reference Rnor_6.0/rn6, to identify brain-specific alternative polyadenylation events in the HXB/BXH recombinant inbred rat panel. Finally, transcripts were filtered based on their expression estimates as determined by RSEM to retain only transcripts with substantial expression in the detected above background (DABG) transcriptome.

Dataset	Transcriptome generation step	Number of genes	Number of transcripts	Transcript:Gene ratio	Number of Ensembl transcripts	Number of StringTie transcripts	Number of aptardi transcripts
Ensembl	Step 1	32,586	40,772	1.25	40,772 (100.0%)	—	—
StringTie	Step 2	33,649	83,920	2.49	40,754 (48.6%)	43,166 (51.4%)	—
Aptardi	Step 3	33,649	155,677	4.63	40,754 (26.2%)	43,166 (27.7%)	71,757 (46.1%)
DABG	Step 4	19,517	59,751	3.06	17,028 (28.5%)	24,219 (40.5%)	18,504 (31.0%)