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

[Dan Bolser]

2009/4/30 Martin Morgan <mtmorgan at fhcrc.org>:
> 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.

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
>>>>>> 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
>>>
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> 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
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
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>