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.
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]]
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James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
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734-615-7826
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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
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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
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