# Custom Genome, Variant calling, RNA-seq

**URL:** <https://help.galaxyproject.org/t/custom-genome-variant-calling-rna-seq/2031>\
**Category:** Uncategorized\
**Tags:** custom-genome\
**Created:** [September 3, 2019, 2:16pm UTC](https://help.galaxyproject.org/t/custom-genome-variant-calling-rna-seq/2031 "2019-09-03T14:16:19Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![AgustinGV](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/agustingv/32/543_2.png) [@AgustinGV](https://help.galaxyproject.org/u/AgustinGV)\
**Post date:** [September 3, 2019, 2:16pm UTC](https://help.galaxyproject.org/t/custom-genome-variant-calling-rna-seq/2031/1 "2019-09-03T14:16:19Z")

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Hi,  
I want to call a variant from a gene on a publicly available data set.  
These are transgenic mice expressing a human transgene not present in rodents.

My plan is to map the read to a human reference genome using STAR and then call variants with FreeBayes. My question is if instead of using a whole reference genome, I can only use Chromosome 22 which is where the gene is.

Is that possible?  
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:** [September 4, 2019, 9:57pm UTC](https://help.galaxyproject.org/t/custom-genome-variant-calling-rna-seq/2031/2 "2019-09-04T21:57:30Z")

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Hello @AgustinGV

I’m not exactly sure what you are trying to do but that you can explain more if needed.

`STAR` will not create a reference assembly.

You can use an existing assembly from your target genome, in whole or in part, as a [Custom Genome/Transcriptome](https://galaxyproject.org/learn/custom-genomes/) to call variants that exist in the RNA-seq dataset. You can also assemble a reference transcriptome.

That said, I would suggest reviewing the publication related to the work you are trying to replicate – what reference did they use? It should be the same in your work or expect different results/statistics.

Please see this related prior Q&A for more options. The tutorials under “Variant Analysis” would also probably apply for your case. [Galaxy tools for the de novo assembled transcriptome annotation](https://help.galaxyproject.org/t/galaxy-tools-for-the-de-novo-assembled-transcriptome-annotation/1988)

Thanks!

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**Author:** ![AgustinGV](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/agustingv/32/543_2.png) [@AgustinGV](https://help.galaxyproject.org/u/AgustinGV)\
**Post date:** [September 4, 2019, 11:21pm UTC](https://help.galaxyproject.org/t/custom-genome-variant-calling-rna-seq/2031/3 "2019-09-04T23:21:34Z")

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Thanks for the answer, my previous post was unclear. I rewrote it for clarity.  
From your answer though I think that what I want to do is called a “custom genome”. I am exploring the tool NormalizeFASTA from the link.

Thank you!

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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:** [April 21, 2026, 12:13am UTC](https://help.galaxyproject.org/t/custom-genome-variant-calling-rna-seq/2031/4 "2026-04-21T00:13:24Z")

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