On Sat, Feb 6, 2010 at 5:13 PM, Martin Morgan <[email protected]> wrote: > Thanks Steve -- there's a single line change to BSgenome (in the early > lines of strand.R) that restores strand levels and behavior to > Rsamtools, but we are still not fully aware of what consequences this > might have for other packages so probably best to stick with your 'last > known good' installation of early January. Certainly your flags should > be parsed correctly.
For what it's worth, I tried simply changing the order of the factors in that BSgenome::strand.R file and ran my tests -- I don't think that solved the problem, though. Take that with a grain of salt, though ... there's a good chance I can be mistaken. I'm debating even sending this email because I'm not sure how thorough I tested that. I quickly looked at some result I expected and it seemed wrong ... As I'm in "mad-dash" mode right now trying to get some things together for a deadline I just took the "nuclear" option and backtracked to earlier revisions of these packages. Once I get out of the woods, I'll be happy to test more thoroughly. I have some samples with sequences that all start with the same 4 NT's on the 5' of the tag (a restriction enzyme was used to cut and create "sequence tags", much like the MPSS protocols of "yore" :-)). I put together some scratch code to test that scenarios (i) and (ii) [from previous email] are kosher for these samples (ie. the correct 4 NT's are the 5' of the sequences in the entire experiment), so I can "easily" check that as soon as I finish this work up. -steve -- 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
