Name
Abstract | ||
|---|---|---|
Paired-end whole transcriptome sequencing provides evidence for fusion transcripts. However, due to the repetitiveness of the transcriptome, many reads have multiple high-quality mappings. Previous methods to find gene fusions either ignored these reads or required additional longer single reads. This can obscure up to 30% of fusions and unnecessarily discards much of the data.We present a method for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing. Using simulated data and data from tumors and cell lines, we show that our method can find fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.A C++ and Python implementation of the method demonstrated in this article is available at http://exon.ucsd.edu/ShortFuse.mckinsel@ucsd.eduSupplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1093/bioinformatics/btr085 | Bioinformatics |
Keywords | Field | DocType |
mapping location,gene fusion,supplementary data,additional single read sequencing,ambiguously mapping,simulated data,previous method,multiple high-quality mapping,paired-end whole transcriptome sequencing,sensitive gene fusion detection,fusion transcript,gene expression profiling,cell line | Gene,Fusion gene,RNA-Seq,Computer science,Exon,Transcriptome,Whole Transcriptome Sequencing,Bioinformatics,Python (programming language),Gene expression profiling | Journal |
Volume | Issue | ISSN |
27 | 8 | 1367-4811 |
Citations | PageRank | References |
12 | 1.64 | 7 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Marcus Kinsella | 1 | 14 | 2.76 |
| Olivier Harismendy | 2 | 43 | 5.92 |
| Masakazu Nakano | 3 | 12 | 1.64 |
| K A Frazer | 4 | 123 | 21.65 |
| Vineet Bafna | 5 | 1967 | 226.80 |