Determine chromosome names in reference genome already in Galaxy?

usegalaxy.org support
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I would like to find out the names of chromosomes contained in one of the Galaxy-provided reference genomes.

Is there a quick and easy way to do that?

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If it’s brought into Galaxy via cvmfs you can check the actual reference files at http://datacache.galaxyproject.org/.

If you’re looking for a (limited) tool-based solution, you could try
https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.9. It works only on the actual fasta reference genomes and does not let you inspect indices for tools though.

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You can also run some simple test mapping against the genome and review the BAM output header. Try a Samtools or Picard stats tool to parse much header information into a tabular report.

Or, if a UCSC-sourced genome, review directly here: https://genome.ucsc.edu. All genomes from this source are exact replicas of the soft-masked genome version. Chromosomes name are in the file chrominfo available from the Table Browser.

FAQ: Mismatched Chromosome identifiers (and how to avoid them)

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