# Determine chromosome names in reference genome already in Galaxy?

**URL:** <https://help.galaxyproject.org/t/determine-chromosome-names-in-reference-genome-already-in-galaxy/1682>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, reference-genome, cvmfs, devops\
**Created:** [July 5, 2019, 8:47am UTC](https://help.galaxyproject.org/t/determine-chromosome-names-in-reference-genome-already-in-galaxy/1682 "2019-07-05T08:47:02Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![aloraine](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/aloraine/32/629_2.png) [@aloraine](https://help.galaxyproject.org/u/aloraine)\
**Post date:** [July 5, 2019, 8:47am UTC](https://help.galaxyproject.org/t/determine-chromosome-names-in-reference-genome-already-in-galaxy/1682/1 "2019-07-05T08:47:02Z")

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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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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [July 5, 2019, 9:50am UTC](https://help.galaxyproject.org/t/determine-chromosome-names-in-reference-genome-already-in-galaxy/1682/2 "2019-07-05T09:50:36Z")

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If it’s brought into Galaxy via cvmfs you can check the actual reference files at [http://datacache.galaxyproject.org/](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](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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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [July 6, 2019, 2:04am UTC](https://help.galaxyproject.org/t/determine-chromosome-names-in-reference-genome-already-in-galaxy/1682/3 "2019-07-06T02:04:47Z")

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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](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)](https://galaxyproject.org/support/chrom-identifiers/)

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 17, 2026, 6:01am UTC](https://help.galaxyproject.org/t/determine-chromosome-names-in-reference-genome-already-in-galaxy/1682/4 "2026-03-17T06:01:44Z")

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