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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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>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 <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/musk.ibms.sinica.edu.tw\/UMARS\/\" ext-link-type=\"uri\">http:\/\/musk.ibms.sinica.edu.tw\/UMARS\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s1-s9","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T20:03:16Z","timestamp":1298059396000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["UMARS: Un-MAppable Reads Solution"],"prefix":"10.1186","volume":"12","author":[{"given":"Sung-Chou","family":"Li","sequence":"first","affiliation":[]},{"given":"Wen-Ching","family":"Chan","sequence":"additional","affiliation":[]},{"given":"Chun-Hung","family":"Lai","sequence":"additional","affiliation":[]},{"given":"Kuo-Wang","family":"Tsai","sequence":"additional","affiliation":[]},{"given":"Chun-Nan","family":"Hsu","sequence":"additional","affiliation":[]},{"given":"Yuh-Shan","family":"Jou","sequence":"additional","affiliation":[]},{"given":"Hua-Chien","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Chun-Hong","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Wen-chang","family":"Lin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,2,15]]},"reference":[{"issue":"3","key":"4367_CR1","doi-asserted-by":"publisher","first-page":"R32","DOI":"10.1186\/gb-2009-10-3-r32","volume":"10","author":"O Harismendy","year":"2009","unstructured":"Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, et al.: Evaluation of next generation sequencing platforms for population targeted sequencing studies. 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