Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

BMC Genomics

Table 2 Results of the de novo assembly using Velvet and Oases

Source	Description	number
Velvet	Contigs	830,469
	Average contig length (bp)	134
Oases	Extended contigs	117,594
	loci	85,555
	loci > 150 bp	56,298
	loci (quality filtered + annotated)	22,117
	Number of unique mappable sheep genes	13,546
	Average annotated contig length (bp)	1,662
NCBI	ovine genbank mRNA entries	4,599
	ovine genes with known mRNA sequence	1,556
	ovine EST entries	325,596
	bovine genbank mRNA entries	43,102
	bovine genes with known mRNA sequence	16,052
Assembly	Total sheep genes with known mRNA sequence	13,987

Following all quality control and filtering steps, there were a total of 24,325 mappable genes. For 21,865 of these genes, positive counts were detected in all 8 lanes, and these genes were used for the further analysis of differential expression. A gene with known mRNA sequence refers to a gene with a gene symbol for which at least one mRNA sequence was found. Note that mRNA sequence entries assigned to hypothetical genes were not included, and that multiple sequence entries were found for some genes. A unique mappable sheep gene refers to a set of one or more Oases loci that could be mapped to a unique gene symbol via BLASTing to sheep, cow, or mouse sequences. The total number of sheep genes with known RNA sequence is derived from the union of de novo assembled genes and previously sequenced genes, 1,115 of which overlapped.

ISSN: 1471-2164