Hi all, I think there might be a bug in Rsamtools. I have reason to believe that the strand information that's being returned from scanBam(...)$strand is flipped, ie. a read that should be on the '+' strand is being reported as aligning to the '-' strand.
Can someone else conform/deny? Thanks, -steve sessionInfo() R version 2.11.0 Under development (unstable) (2009-12-28 r50849) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_0.1.28 BSgenome_1.15.4 Biostrings_2.15.19 IRanges_1.5.39 loaded via a namespace (and not attached): [1] Biobase_2.7.0 -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
