[Gmod-help] Fwd: Pipelines for 'short read processing' + chado back-end?

[Dan Bolser]

:-)


---------- Forwarded message ----------
From: Dan Bolser <dan.bolser at gmail.com>
Date: 2009/8/25
Subject: Pipelines for 'short read processing' + chado back-end?
To: gmod-schema at lists.sourceforge.net


Hi all,

My colleagues are meeting on Thursday to discuss the design of a
database schema to handle data from various Next Generation Sequencing
(NGS) experiments. The lab I work in is expecting to receive short
read Illumina / Solexa data from: transcriptomics / SAGE / RNAseq,
ChIP-seq, and miRNA-seq.

In all cases we expect our 'analysis pipeline' to map reads onto a
reference sequence or database of sequences, and store the result in a
database to facilitate various downstream 'analysis'. In addition to
the mapping results, we need to store experimental meta-data and
mapping meta-data.

Is there a list of Chado usage examples that demonstrate handling
these kinds of data? I have already suggested that Chado may be worth
'evaluation', however, I'd like to be able to show them some concrete
examples.

Thanks very much for any information on the above.

All the best,
Dan.