title: Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length.
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.
authors: School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.
authors: Shao-Ke
authors: SK
authors: Lou
authors: Jing-Woei
authors: JW
authors: Li
authors: Hao
authors: H
authors: Qin
authors: Aldrin Kay-Yuen
authors: AK
authors: Yim
authors: Leung-Yau
authors: LY
authors: Lo
authors: Bing
authors: B
authors: Ni
authors: Kwong-Sak
authors: KS
authors: Leung
authors: Stephen Kwok-Wing
authors: SK
authors: Tsui
authors: Ting-Fung
authors: TF
authors: Chan
mesh_terms: D000818:Animals; D015870:Gene Expression; D016678:Genome; D006801:Humans; D007438:Introns; D016013:Likelihood Functions; D012326:RNA Splicing; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D016008:Statistical Distributions