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

[Dan Bolser]

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.


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
>