[Bioc-sig-seq] SOLID data

[Martin Morgan]

Hi Nicolas --

nicolas servant <Nicolas.Servant at curie.fr> writes:

> Dear List,
>
> Does anybody have ever try to analyse some SOLID data using Biostrings
> and ShortRead ?? or anything else !
> The ShortRead package was developped to manipulate short reads from
> Solexa, 454, Helicos or SOLiD (cf vignette), but in practice, it seems

A not necessarily helpful answer; maybe others will reply, but... I
removed SOLiD from explicit mention in the ShortRead vignette, because
as you say the color space model complicates things (the vignette was
written early in the life of ShortRead, when plans ran ahead of
reality). ShortRead I/O and other Bioconductor tools might still be
helpful at some point in a SOLiD work flow, once reads are represented
as traditional nucleotide sequences (which I guess they must be at
some point?).

Martin

> to be more complicated ... the input are different from Solexa of
> course, and we have to deal with the color code ...
> Does anybody have some experience with this data ? especially for the
> adaptor removal ?
>
> Thanks,
> Nicolas
>
> -- 
> Nicolas Servant
> Equipe Bioinformatique
> Institut Curie
> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE
>
> Email: Nicolas.Servant at curie.fr
> Tel: 01 56 24 69 85
> http://bioinfo.curie.fr/
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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