{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T07:25:20Z","timestamp":1648625120900},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s5-s2","type":"journal-article","created":{"date-parts":[[2011,8,3]],"date-time":"2011-08-03T08:09:10Z","timestamp":1312358950000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length"],"prefix":"10.1186","volume":"12","author":[{"given":"Shao-Ke","family":"Lou","sequence":"first","affiliation":[]},{"given":"Jing-Woei","family":"Li","sequence":"additional","affiliation":[]},{"given":"Hao","family":"Qin","sequence":"additional","affiliation":[]},{"given":"Aldrin Kay-Yuen","family":"Yim","sequence":"additional","affiliation":[]},{"given":"Leung-Yau","family":"Lo","sequence":"additional","affiliation":[]},{"given":"Bing","family":"Ni","sequence":"additional","affiliation":[]},{"given":"Kwong-Sak","family":"Leung","sequence":"additional","affiliation":[]},{"given":"Stephen Kwok-Wing","family":"Tsui","sequence":"additional","affiliation":[]},{"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,7,27]]},"reference":[{"issue":"5","key":"4659_CR1","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1038\/nrm1645","volume":"6","author":"AJ Matlin","year":"2005","unstructured":"Matlin AJ, Clark F, Smith CWJ: Understanding alternative splicing: towards a cellular code. 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