2009/4/30 Martin Morgan <[email protected]>: > Dan Bolser wrote: >> >> 2009/4/30 James W. MacDonald <[email protected]>: >>> >>> Dan Bolser wrote: >>>> >>>> 2009/4/27 James W. MacDonald <[email protected]>: >>>>> >>>>> There is some older information from BioC2008 here (starting on page >>>>> 12): >>>>> >>>>> >>>>> >>>>> http://www.bioconductor.org/workshops/2008/BioC2008/labs/PairwiseSequenceAlignments/Alignments.pdf >>>>> >>>>> Or you could search the Bioc-sig-seq listserv for newer information: >>>>> >>>>> >>>>> >>>>> http://www.google.com/search?hl=en&as_q=adapter&as_epq=&as_oq=&as_eq=&num=10&lr=&as_filetype=&ft=i&as_sitesearch=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fbioc-sig-sequencing%2F&as_qdr=all&as_rights=&as_occt=any&cr=&as_nlo=&as_nhi=&safe=images >>>> >>>> Is there a wiki where this info gets logged? >>> >>> Unfortunately, no (or fortunately, if you are the person charged with >>> updating the wiki). We have dabbled a bit with using a wiki to track >>> information or certain long-running discussions, but it's like having a >>> microwave at work - most people want to use it, but nobody has the time >>> or >>> inclination to keep it clean. >> >> Good analogy ;-) >> >> >>> Fortunately there are many people who subscribe to the various BioC lists >>> who are more than helpful, and our friend google is really good at >>> finding >>> their responses, given the correct search string. So we rely on the list >>> archives as the primary store of information rather than a wiki. >> >> >> Yeah, but for simple 'how-to's and the like, I love to have dedicated >> categorized pages. My personal approach is to keep rough notes when >> learning a new package, and it would be easy to do that on a wiki. The >> resulting 'log' could then be tidied up into a (series of) simple >> 'how-to's. I know it doesn't sound like much, but at least seeing the >> functions that people use in use can be a big help to learning. >> >> I'll try to log some of my explorations somewhere on bioinformatics.org or >> OWW. > > I think ideally vignettes represent accumulated wisdom on 'how-to', so the > 'in-project' way of doing this is to (suggesting to the package maintainer, > if necessary) update the relevant vignette. Probably the issue is that as > information / simple tasks accumulate one faces the task of navigating > increasingly daunting documentation. Certainly navigating complex docs on > the web can be facilitated by searches, hyperlinks, etc., and an interesting > direction might be to produce the vignettes as HTML documents in addition to > pdf. In some ways latex2HTML might be a very straight-forward way of doing > this.
I think that would be a step in the right direction. > > Martin > >> >> Cheers, >> Dan. >> >> >>> Best, >>> >>> Jim >>> >>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> Xiang Xu wrote: >>>>>> >>>>>> Hello all, >>>>>> >>>>>> Is there someone can show me some software or tools for trimming the >>>>>> adaptors of Solexa short reads? Do you have any protocol for analysis >>>>>> sequencing data of gene expression and small RNA? >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Xiang Xu >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-sig-sequencing mailing list >>>>>> [email protected] >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>>> >>>>> -- >>>>> James W. MacDonald, M.S. >>>>> Biostatistician >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> >>>>> _______________________________________________ >>>>> Bioc-sig-sequencing mailing list >>>>> [email protected] >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
