Hi all, I want to get the uniquely mapping reads from an object of AlignedRead class. How can I do this? Thanks. -- Likun Wang MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China Tel: +86-10-62794294 Fax: +86-10-62786911 Email: wang.likun at gmail.com

Likun Wang wrote: > Hi all, > I want to get the uniquely mapping reads from an object of AlignedRead class. > How can I do this? It depends a little on what you mean by 'uniquely aligning', e.g., identical sequence, identical + / - strand, overlap of identical nucleotides. You can try aln[uniqueFilter()(aln)] or if that is not to your liking specify your own criteria for subsetting, u <- !duplicated(position(aln)) & !duplicated(chromosome(aln)) aln[u] Martin > Thanks. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793