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SUMMARY:Virtual BSU seminar: &quot\;NanoSplicer: Accurate identification o
 f splice junctions using Oxford Nanopore sequencing&quot\; - Dr Heejung Sh
 im\, Melbourne Integrative Genomics (MIG)\, University of Melbourne
DTSTART:20211102T100000Z
DTEND:20211102T110000Z
UID:TALK164356@talks.cam.ac.uk
CONTACT:Alison Quenault
DESCRIPTION:Nanopore sequencing by Oxford Nanopore Technologies is a long-
 read sequencing method that has considerable advantages for characterising
  RNA isoforms. It works by recording changes in electrical current when a 
 DNA or RNA molecule traverses through a pore. However\, basecalling of thi
 s raw signal (known as a squiggle) is error prone\, making it challenging 
 to accurately identifying splice junctions. Existing strategies include us
 ing matched short-read data and/or annotated splice junctions to correct s
 plice junctions from mapped nanopore reads\, but add expense or limit junc
 tions to known (incomplete) annotations. Therefore\, a method that could a
 ccurately identify splice junctions solely from nanopore data would have n
 umerous advantages.\n \nIn this talk\, I will present a method ``NanoSplic
 er'' that exploits the information in raw nanopore signals (squiggles) to 
 improve splice junction identification. The key idea is to identify\, for 
 each splice junction\, which of the squiggles predicted from potential spl
 ice junction sequences best matches the observed junction squiggle. This e
 nables NanoSplicer to identify splice junctions solely from the nanopore d
 ata and its performance to be independent of other reads or read depth\, h
 aving the potential to better identify rare splice junctions. Using both s
 ynthetic and biological data\, we demonstrate that NanoSplicer improves sp
 lice junction identification\, especially when the basecalling error rate 
 near the splice junction is elevated. \n \nThis is a joint work with Yupei
  You and Michael Clark at the University of Melbourne.\n
LOCATION:Virtual Seminar 
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