Hi Jen,

Many thanks for this, on a related subject do you know of a way to correct a FASTA file on the basis of a pileup (or even just on the BAM file)?

Best Wishes,

Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol

Tel. +44 117 3312058
Fax. +44 117 3312091

On 25 Jul 2011, at 17:52, Jennifer Jackson wrote:

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).


Hopefully this helps,

Galaxy team

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

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


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