L_RNA_scaffolder: scaffolding genomes with transcripts

BMC Genomics

Table 1 Comparing L_RNA_scaffolder results with Zv_9 assembly

Type			Number
(i) Consistent	Both order and orientation were consistent		5,980
(ii) Inversions	More evidence for L_RNA_scaffolder^a		20
	More evidence for Zv_9^b		0
			20
(iii) Relocations	Correctable relocations		885
	Errant relocations	More evidence for L_RNA_scaffolder	98
		More evidence for Zv_9	21
		Uncertain^c	102
			1,106
(iv) Translocations	More evidence for L_RNA_scaffolder		43
	More evidence for Zv_9		16
	Uncertain		33
	Contigs from two reference scaffolds		31
	Contigs from one scaffold and one chromosome, respectively		137
			260
Total			7,366

^a Three approaches including syntenic block orders, human homolog coverage and zebrafish ‘guide’ transcript completeness, are used to determine the correct connection. The connection with the most evidence is regarded to be correct. For these cases, L_RNA_scaffolder results have more supporting evidence than Zv_9.
^b For these cases, Zv_9 connections have more supporting evidence than L_RNA_scaffolder results.
^c There is the same amount of evidence or no supporting evidence for both conflicting connections. It is hard to determine which connection is correct.

ISSN: 1471-2164