期刊
SCIENCE CHINA-LIFE SCIENCES
卷 54, 期 12, 页码 1129-1133出版社
SCIENCE PRESS
DOI: 10.1007/s11427-011-4256-9
关键词
RNA-Seq; de novo transcriptome assembly; next generation sequencing
类别
资金
- National Basic Research Program of China [2010CB945401, 2007CB108800]
- National Natural Science Foundation of China [30870575, 31071162, 31000590]
- Science and Technology Commission of Shanghai Municipality [11DZ2260300]
De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences. We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line, respectively. We then determined an efficient way to yield an optimal overall assembly using three different strategies. We first assembled brain and cell line transcriptome using a single k-mer length. Next we tested a range of values of k-mer length and coverage cutoff in assembling. Lastly, we combined the assembled contigs from a range of k values to generate a final assembly. By comparing these assembly results, we found that using only one k-mer value for assembly is not enough to generate good assembly results, but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据