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ShortRead with BWA
2010 Apr 27
2
ShortRead with BWA
...ng with ShortRead, I found a document (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention that readAligned was extended to support SAM format (for example, BWA output). So I tried readAligned with BWAAln <- readAligned(BWAFile, type = "BWA") but then I got error: > BWAAln <- readAligned(BWAFile, type = "BWA") Error: UserArgumentMismatch arugment 'type' had value 'BWA' allowable values: 'SolexaExport' 'SolexaAlign' 'SolexaPrealign' 'SolexaRe...