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

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

Sample Original read typea Published transcriptomes Reciprocally re-annotated transcriptomes
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
  1. a Reads originally 100 bp paired-end (PE) were split in half to be 50 bp each and treated as single-end (SE) reads