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Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length.
- Source :
-
BMC bioinformatics [BMC Bioinformatics] 2011; Vol. 12 Suppl 5, pp. S2. Date of Electronic Publication: 2011 Jul 27. - Publication Year :
- 2011
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Abstract
- Background: RNA sequencing (RNA-seq) measures gene expression levels and permits splicing analysis. Many existing aligners are capable of mapping millions of sequencing reads onto a reference genome. For reads that can be mapped to multiple positions along the reference genome (multireads), these aligners may either randomly assign them to a location, or discard them altogether. Either way could bias downstream analyses. Meanwhile, challenges remain in the alignment of reads spanning across splice junctions. Existing splicing-aware aligners that rely on the read-count method in identifying junction sites are inevitably affected by sequencing depths.<br />Results: The distance between aligned positions of paired-end (PE) reads or two parts of a spliced read is dependent on the experiment protocol and gene structures. We here proposed a new method that employs an empirical geometric-tail (GT) distribution of intron lengths to make a rational choice in multireads selection and splice-sites detection, according to the aligned distances from PE and sliced reads.<br />Conclusions: GT models that combine sequence similarity from alignment, and together with the probability of length distribution, could accurately determine the location of both multireads and spliced reads.
Details
- Language :
- English
- ISSN :
- 1471-2105
- Volume :
- 12 Suppl 5
- Database :
- MEDLINE
- Journal :
- BMC bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 21988959
- Full Text :
- https://doi.org/10.1186/1471-2105-12-S5-S2