is there any way to read Bowtie alignment results into R automatically ?
specially i want alignment location and sequences in r
Are your alignments in BAM format?
yes. SAM and BAM..
Have you looked at the QuasR package (http://www.bioconductor.org/packages/release/bioc/vignettes/QuasR/inst/doc/QuasR.pdf, page 13, "using external BAM files)
See the GenomicAlignments package.
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