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 <[email protected]>
Subject: [Bioc-sig-seq] SOLID data
To: [email protected]
Message-ID: <[email protected]>
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
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