[Bioc-sig-seq] SOLID data

[rcaloger]

Hi,

I am working with SOLID data essentially to make quantification of 
non-coding trasncriptome.
Due to the peculiar characteristics of SOLID data I decided to use a 
software born for SOLID data mapping: SOCS, Ondov et al. Bioinformatics 
2008 (http://bioinformatics.oxfordjournals.org/cgi/content/short/btn512v1).
My idea is to use SOCS outputs as stating material to be handled in 
Bioconductor/R. Therefore, I am writing a package that runs SOCS and 
uses its outputs to make quantitative analyses.
Unfortuantely it is not mature enough to be submitted to Bioconductor.
Raffaele

> Message: 1
> Date: Wed, 04 Feb 2009 15:49:10 +0100
> From: nicolas servant <Nicolas.Servant at curie.fr>
> Subject: [Bioc-sig-seq] SOLID data
> To: bioc-sig-sequencing at r-project.org
> Message-ID: <4989AAE6.7060302 at curie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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 
> 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
>
>