Table 1

Comparison of transcriptome datasets as a reference for RNA-Seq analysis
Developmental stage Counted reads Genoscope 8x (30434 transcripts) Genoscope 12x (26346 transcripts) NCBI RefSeq (23720 transcripts)
Young berries 32 283 153 17 127 563 (53.0) 16 340 511 (50.6) 24 972 894 (77.3)
Early-veraison 36 280 465 21 111 334 (58.2) 22 423 774 (56.6) 30 695 559 (84.6)
Late-veraison 38 434 765 23 572 898 (61.3) 22 522 747 (58.6) 33 605 499 (87.4)
Ripe berries 41 947 022 24 606 233 (59.6) 25 516 490 (58.1) 35 251 865 (85.4)
Total 148 945 405 86 418 028 (58.0) 86 803 522 (58.3) 124 525 817 (83.6)

Number of Illumina HiSeq sequencing reads from each developmental stage mapped to selected reference mRNA transcript collections. The percentage of counted reads that were mapped is presented in parenthesis.

Sweetman et al.

Sweetman et al. BMC Genomics 2012 13:691   doi:10.1186/1471-2164-13-691

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