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Old 07-28-2010, 10:17 AM   #1
krobison
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Default Programmatic querying of ENA?

The SRAdb module for R/BioConductor is a nifty way to query metadata for the NCBI Short Read Archive using SQL.

Is there a similar tool out there fore the EBI's similar ENA or the DDBJ's Sequence Read Archive? Or better yet, a way to slurp all three databases into a common relational schema?
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Old 07-29-2010, 07:02 AM   #2
maubp
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I assumed the 3 short read archives exchanged data and are effectively in sync with each other (perhaps with some time delay). Is that not so?
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Old 07-29-2010, 10:18 AM   #3
krobison
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I think you are right -- but not clear what the time delay is. Definitely I could yesterday find something in ENA not in NCBI SRA; perhaps I'll check each day to see if it has shown up!
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Old 09-06-2012, 03:49 AM   #4
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Does anybody know how to make effective text searches at ENA or SRA? I am looking for sequencing projects (whole-genome or exome) on the Illumina platform. The primary species in mind is humans, but mice or other creatures might be interesting too. The coverage should be high (>= 10x).
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