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Table 2 Reference transcriptome sequence, genome sequence and annotation versions accessed from Ensembl, where the Version id suffix shows the Ensembl version

From: ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs

Reference

Total

Expressed

Species

Version id

Genes

Isoforms

Genes

Isoforms

Human

GRCh38.99

40,491

1,904,32

22,510

1,02,552

Mouse

GRCm38.99

36,711

1,19,353

17,400

52,845

Arabid.

TAIR10.48

27,655

48,359

23,085

38,004

Rice

IRGSP-1.0.48

37,967

44,761

29,703

34,956

Zeb.fish

GRCz11.99

30,628

57,775

23,963

35,189

Poplar

Pop_tri_v3.46

41,335

73,012

29,400

44,652

  1. The number of genes and isoforms are counted from the reference transcriptome. Genes and isoforms are considered expressed if TPM>0 as calculated by RSEM on the datasets in Table 1
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BMC Bioinformatics

ISSN: 1471-2105

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