Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
Ashish Agarwal1, David Koppstein, Joel Rozowsky
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
BMC Genomics
|June 23, 2010
Summary
RNA-Seq offers higher accuracy in exon boundary detection and dynamic range compared to tiling arrays. Researchers should choose between RNA-Seq and tiling arrays based on their specific transcriptome analysis needs.
Area of Science:
- Genomics
- Transcriptomics
- Molecular Biology
Background:
- Tiling arrays have been widely used for transcriptome analysis without prior assumptions.
- RNA sequencing (RNA-Seq) is emerging as a cost-effective alternative for transcriptome profiling.
Purpose of the Study:
- To compare the performance of tiling arrays and RNA-Seq for transcriptome analysis.
- To guide researchers in selecting the optimal technology for their specific needs.
Main Methods:
- Comparative analysis of tiling array and RNA-Seq data from C. elegans poly(A)-enriched RNA.
- Assessment of exon boundary detection, dynamic range, and sensitivity as a function of sequencing depth.
- Analysis of cross-hybridization effects on tiling arrays and development of a "black list" strategy.
Main Results:
- RNA-Seq demonstrates superior performance in exon boundary detection and dynamic range compared to tiling arrays.
- Approximately 4 million RNA-Seq reads are needed to match the sensitivity of two tiling array replicates.
- A method for identifying unreliable "black list" regions on tiling arrays due to cross-hybridization was developed.
Conclusions:
- RNA-Seq provides greater accuracy for specific transcriptome analysis aspects, while tiling arrays offer lower cost for broad detection.
- Careful selection of either tiling arrays or RNA-Seq is crucial, depending on the biological investigation.
- Ongoing advancements in sequencing technology necessitate continuous re-evaluation of these platforms.
