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Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
- Source :
- Scientific Reports, Vol 7, Iss 1, Pp 1-10 (2017), Scientific Reports
- Publication Year :
- 2017
- Publisher :
- Springer Science and Business Media LLC, 2017.
-
Abstract
- Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers. Combining the experimental and computational advancements, our solution is comparable with the bulk mRNA-seq in quantification, reliably detects splice junctions and minimizes the bias with much less mappable reads.
- Subjects :
- 0301 basic medicine
Genetics
Multidisciplinary
Sequence Analysis, RNA
Gene Expression Profiling
Science
Low input
Computational Biology
RNA-Seq
Ion semiconductor sequencing
Biology
Article
03 medical and health sciences
030104 developmental biology
Semiconductors
Mapping algorithm
Costs and Cost Analysis
Medicine
splice
Throughput (business)
Algorithm
Reference genome
Subjects
Details
- ISSN :
- 20452322
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- Scientific Reports
- Accession number :
- edsair.doi.dedup.....69bd2dd874ac0c66395c5200fcb1e39a