title: UMARS: Un-MAppable Reads Solution.
abstract: BACKGROUND
  Un-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequencing (NGS) technology has emerged as a powerful tool for generating high-throughput sequencing data and has been applied to many kinds of biological research. In a typical analysis, adaptor-trimmed NGS reads were first mapped back to reference sequences, including genomes or transcripts. However, a fraction of NGS reads failed to be mapped back to the reference sequences. Such un-mappable reads are usually imputed to sequencing errors and discarded without further consideration.
  
  
  METHODS
  We are investigating possible biological relevance and possible sources of un-mappable reads. Therefore, we developed UMARS to scan for virus genomic fragments or exon-exon junctions of novel alternative splicing isoforms from un-mappable reads. For mapping un-mappable reads, we first collected viral genomes and sequences of exon-exon junctions. Then, we constructed UMARS pipeline as an automatic alignment interface.
  
  
  RESULTS
  By demonstrating the results of two UMARS alignment cases, we show the applicability of UMARS. We first showed that the expected EBV genomic fragments can be detected by UMARS. Second, we also detected exon-exon junctions from un-mappable reads. Further experimental validation also ensured the authenticity of the UMARS pipeline. The UMARS service is freely available to the academic community and can be accessed via http://musk.ibms.sinica.edu.tw/UMARS/.
  
  
  CONCLUSIONS
  In this study, we have shown that some un-mappable reads are not caused by sequencing errors. They can originate from viral infection or transcript splicing. Our UMARS pipeline provides another way to examine and recycle the un-mappable reads that are commonly discarded as garbage.
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Sung-Chou
authors.initials: SC
authors.lastname: Li
authors.forename: Wen-Ching
authors.initials: WC
authors.lastname: Chan
authors.forename: Chun-Hung
authors.initials: CH
authors.lastname: Lai
authors.forename: Kuo-Wang
authors.initials: KW
authors.lastname: Tsai
authors.forename: Chun-Nan
authors.initials: CN
authors.lastname: Hsu
authors.forename: Yuh-Shan
authors.initials: YS
authors.lastname: Jou
authors.forename: Hua-Chien
authors.initials: HC
authors.lastname: Chen
authors.forename: Chun-Hong
authors.initials: CH
authors.lastname: Chen
authors.forename: Wen-Chang
authors.initials: WC
authors.lastname: Lin
mesh_terms: D002874:Chromosome Mapping; D018076:DNA, Complementary / Q000235:genetics; D005091:Exons; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012326:RNA Splicing; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D018076:DNA, Complementary