Following a recent thread, I also have found convenient to store nextgen
data as RangedData instead of ShortRead objects. They require far less
memory and make feasible working with several samples at the same time (in
my 8Gb RAM desktop I can load 2 ShortRead objects at the most, with
RangedData I haven't struck the upper limit yet).

I am thinking about taking this idea a step forward: RangedDataList allows
storing info from several samples (e.g. IP and control) in a single object.
The only problem is RangedDataList does not store information about the
samples, e.g. the phenoData we're used to in ExpressionSet objects. My idea
is to define something like a "SequenceSet" class, which would contain a
RangedDataList with the ranges, a phenoData with sample information, and
possibly also information about the experiment (e.g. with the MIAME analog
for sequencing, MIASEQE).

The thing is I don't want to re-invent the wheel. I haven't seen that this
is implemented yet, but is someone working on it? Any criticism/ ideas?

Best,

David

-- 
David Rossell, PhD
Manager, Bioinformatics and Biostatistics unit
IRB Barcelona
Tel (+34) 93 402 0217
Fax (+34) 93 402 0257
http://www.irbbarcelona.org/bioinformatics

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