Hello David,

To calculate coverage, please see the tool "Regional Variation -> Feature coverage". Query and target must both be in Interval/BED format. Query data in Interval/BED format is possible in most of the dataflow paths through the tools and from external sources. The reference genome file will likely need to be imported and formatted.

This is simple example history where I pulled the chromInfo file from UCSC and formatted, extracted a subset of genes in BED format, and ran the "Feature Coverage" tool (both directions, see datasets 8 and 9).

http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/galaxy-user-calculating-percent-coverage-over-the-target-genome-7-22

Hopefully this helps,

Jen
Galaxy team

On 7/22/11 12:32 PM, David Matthews wrote:

Hi

Does anyone know how to calculate how much of a genome was covered by an alignment irrespective of the depth at each base?

Cheers

David

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