# Request --Index Arabidopsis thaliana TAIR 10 for HISAT2/Usegalaxy.org, Solution -- Use a Custom Genome or Usegalaxy.eu

**URL:** <https://help.galaxyproject.org/t/request-index-arabidopsis-thaliana-tair-10-for-hisat2-usegalaxy-org-solution-use-a-custom-genome-or-usegalaxy-eu/1508>\
**Category:** usegalaxy.org support\
**Tags:** reference-index\
**Created:** [June 8, 2019, 3:51am UTC](https://help.galaxyproject.org/t/request-index-arabidopsis-thaliana-tair-10-for-hisat2-usegalaxy-org-solution-use-a-custom-genome-or-usegalaxy-eu/1508 "2019-06-08T03:51:46Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Matt\_Escobar](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/matt_escobar/32/660_2.png) [@Matt\_Escobar](https://help.galaxyproject.org/u/Matt_Escobar)\
**Post date:** [June 8, 2019, 3:51am UTC](https://help.galaxyproject.org/t/request-index-arabidopsis-thaliana-tair-10-for-hisat2-usegalaxy-org-solution-use-a-custom-genome-or-usegalaxy-eu/1508/1 "2019-06-08T03:51:46Z")

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Hello,

Would it be possible for you to add the Arabidopsis thaliana TAIR 10 genome to the list of built-in references for HISAT2?

Thanks,  
Matt

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**Author:** ![Sammy](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sammy/32/445_2.png) [@Sammy](https://help.galaxyproject.org/u/Sammy)\
**Post date:** [June 11, 2019, 12:19pm UTC](https://help.galaxyproject.org/t/request-index-arabidopsis-thaliana-tair-10-for-hisat2-usegalaxy-org-solution-use-a-custom-genome-or-usegalaxy-eu/1508/2 "2019-06-11T12:19:50Z")

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Hey Matt,

Why do you want to add the genome to the built in genome?

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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:** [June 11, 2019, 5:57pm UTC](https://help.galaxyproject.org/t/request-index-arabidopsis-thaliana-tair-10-for-hisat2-usegalaxy-org-solution-use-a-custom-genome-or-usegalaxy-eu/1508/3 "2019-06-11T17:57:15Z")

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Hi,

Some consolidation of reference genome, reference annotation, and associated indexes will be done between the usegalaxy.\* servers, likely sometime this year.

- `TAIR10` is already on the list to be indexed for `HISAT2` at **Galaxy Main** [https://usegalaxy.org](https://usegalaxy.org).\* The version already available/indexed for some tools is from [UCSC](http://genome.ucsc.edu/), so that is where you should also get the fasta for the genome if you decided to use the Custom Genome functions. Annotation would be best if sourced from [iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).

- `TAIR10` is already indexed for `HISAT2` at **Galaxy EU** [https://usegalaxy.eu](https://usegalaxy.eu).\* This is also the UCSC version. iGenomes is still the best annotation source.

Custom Genome FAQ plus how to avoid chromosome mismatches when incorporating reference annotation (will probably be needed at either server).

- [Preparing and using a Custom Reference Genome or Build](https://galaxyproject.org/learn/custom-genomes/)
- [Mismatched Chromosome identifiers (and how to avoid them)](https://galaxyproject.org/support/chrom-identifiers/)

Related Q&A that explains more about how to get `iGenome` annotation into Galaxy and avoid any content-level mismatch problems: [What exactly are the "built-in references" in Galaxy's HISAT2?](https://help.galaxyproject.org/t/what-exactly-are-the-built-in-references-in-galaxys-hisat2/789)

Thanks!

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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:** [December 20, 2023, 12:37am UTC](https://help.galaxyproject.org/t/request-index-arabidopsis-thaliana-tair-10-for-hisat2-usegalaxy-org-solution-use-a-custom-genome-or-usegalaxy-eu/1508/4 "2023-12-20T00:37:40Z")

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