I'm just thinking out loud about how to incorporate high throughput
transcriptome sequencing data into BASE.  It's some way off, but I'm assuming
that it will be cheap and quantitative enough to replace arrays at some point
during the renewal period of our project (2009-2014).

1. Create an "array design" with all genes of interest (ideally this would be
   the largest set possible, e.g. known genes + predicted genes of all
   qualities, perhaps even predicted genes from the new sequence data).  The
   layout would be fictitious, of course (what's the minimum one can get away

2. Create a rawbioassay to correspond to each sequencing run.

Then *one* of 3a/b/c for each sequencing run/rawbioassay:

3a. Outside BASE, align the new sequences to genome or transcript sequences
    and calculate "intensities" for each gene on the "array design" and dump
    into a tab delimited raw data file.  Attach that file to the rawbioassay
    and import numeric data as usual.

3b. Upload the text file of sequences to the raw bioassay's "data file".
    Create a BASE plugin to do the the alignment and quantification as in 3a,
    and load the numeric data into the database.

3c. Similar to 3b, but calculate the intensities at the "create root bioassay"
    step, similar to the Affymetrix RMA plugin.

4. continue with analysis as normal.  biosources, samples etc can be linked to
   the bioassay too, of course.

I guess a new raw data type (for "Generic" platform) would have to be
created for 3a (and 3b?) but that's not difficult.

Is it possible to go with 3a, but also attach the sequence file to the raw
bioassay (or scan?) - something like keeping tiff files for scans?  Just for
documentation purposes.

Any thoughts from the community or developers?


Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]

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