A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species

Table 4 | List of RNA-seq samples and the percentage and number of mapped reads to different reference transcriptomes

Sample	Original read type^a	Published transcriptomes		Reciprocally re-annotated transcriptomes
Sample	Original read type^a	Percentage	Total number of mapped reads	Percentage	Total number of mapped reads
D. melanogaster replicate A	SE 50 bp	58.86 %	28,486,024	57.33 %	27,744,730
D. melanogaster replicate B	SE 50 bp	44.23 %	17,675,472	43.19 %	17,260,775
D. melanogaster replicate C	SE 50 bp	65.51 %	25,316,846	63.91 %	24,699,746
D. mauritiana replicate A	SE 50 bp	40.70 %	16,575,011	43.31 %	17,639,874
D. mauritiana replicate B	SE 50 bp	56.17 %	31,884,442	60.07 %	34,100,435
D. mauritiana replicate C	SE 50 bp	53.01 %	23,653,723	56.98 %	25,425,486
D. mauritiana replicate D	PE 100 bp	56.06 %	111,643,922	61.07 %	121,610,905
D. mauritiana replicate E	PE 100 bp	54.28 %	130,638,956	59.51 %	143,226,939
D. mauritiana replicate F	PE 100 bp	60.90 %	144,541,354	66.21 %	157,165,639
D. simulans replicate A	PE 100 bp	62.26 %	118,272,529	66.71 %	126,741,807
D. simulans replicate B	PE 100 bp	57.90 %	138,364,665	62.56 %	149,508,494
D. simulans replicate C	PE 100 bp	56.32 %	150,692,651	60.98 %	163,168,587

^a Reads originally 100 bp paired-end (PE) were split in half to be 50 bp each and treated as single-end (SE) reads

ISSN: 1471-2164