Please use this identifier to cite or link to this item:
http://hdl.handle.net/20.500.11861/7534
Title: | Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length |
Authors: | Lou, Shao-Ke Li, Jing-Woei Qin, Hao Yim, Aldrin K Lo, Leung-Yau Ni, Bing Prof. LEUNG Kwong Sak Tsui, Stephen K. Chan, Ting-Fung |
Issue Date: | 2011 |
Source: | BMC Bioinformatics, 2011, Vol. 12, Issue SUPPL.527, Article number S2 |
Journal: | BMC Bioinformatics |
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.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.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. © 2011 Lou et al; licensee BioMed Central Ltd. |
Type: | Peer Reviewed Journal Article |
URI: | http://hdl.handle.net/20.500.11861/7534 |
ISSN: | 14712105 |
DOI: | 10.1186/1471-2105-12-S5-S2 |
Appears in Collections: | Applied Data Science - Publication |
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