search for: readalign

...uencing project, and heard about R as well as some of its packages for next gen sequencing, and decided to give it a try. Starting 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...

Hi, I want to group a large list (20 million) of strings into categories based on string similarity? The specific problem is: given a list of DNA sequence as below ACTCCCGCCGTTCGCGCGCAGCATGATCCTG ACTCCCGCCGTTCGCGCGCNNNNNNNNNNNN CAGGATCATGCTGCGCGCGAACGGCGGGAGT CAGGATCATGCTGCGCGCGAANNNNNNNNNN CAGGATCATGCTGCGCGCGNNNNNNNNNNNN ...... ..... NNNNNNNCCGTTCGCGCGCAGCATGATCCTG