[Bioc-sig-seq] About trimming adaptor of Solexa short reads

[Martin Morgan]

Dan Bolser wrote:
> 2009/4/30 James W. MacDonald <jmacdon at med.umich.edu>:
>>
>> Dan Bolser wrote:
>>> 2009/4/27 James W. MacDonald <jmacdon at med.umich.edu>:
>>>> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-sig-sequencing mailing list
>>>>> Bioc-sig-sequencing at r-project.org
>>>>> 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
>>>> Bioc-sig-sequencing at r-project.org
>>>> 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
>>
> 
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> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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