# Inquiry about lettuce genome

**URL:** <https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608>\
**Category:** Resources\
**Tags:** reference-index, custom-genome, reference-annotation, reference-genome, custom-build, resources\
**Created:** [October 5, 2024, 2:47pm UTC](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608 "2024-10-05T14:47:06Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Kelvin](https://avatars.discourse-cdn.com/v4/letter/k/7ba0ec/32.png) [@Kelvin](https://help.galaxyproject.org/u/Kelvin)\
**Post date:** [October 5, 2024, 2:47pm UTC](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608/1 "2024-10-05T14:47:06Z")

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Hello,  
I want to ask if galaxy has lettuce reference genome. I’m considering using galaxy for my RNA-seq project in lettuce. 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:** [October 7, 2024, 5:05pm UTC](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608/2 "2024-10-07T17:05:50Z")

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Welcome, @Kelvin

You will need to find the assembled reference genome, and any available reference annotation for it, and load those files into Galaxy. You can then use the genome as a **Custom Reference Genome** with tools. This works the same as an index natively available on the server.

Start here → [FAQ: How to use Custom Reference Genomes?](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html)

Similar Q&A at this forum involving that functionality can be found at the #custom-genome tag.

And we have tutorials here → [Transcriptomics / Tutorial List](https://training.galaxyproject.org/training-material/topics/transcriptomics/)

From just a quick search I found the genome resource here → [Lactuca sativa genome assembly Lsat\_Salinas\_v11 - NCBI - NLM](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002870075.4/)

As someone who interned at the USDA in Salinas, CA 30 years ago, attempting to sequence the _Lactuca sativa_ genome via PCR, your question made me smile!! Happy science! 🙂

I usually don’t do this, but as a test and example, I copied the correct URLs from [the FTP site](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/870/075/GCF_002870075.4_Lsat_Salinas_v11/) (link is in a tab at the top) into a history using the **Upload** tool with all defaults. I then standardized the format of both so that these will work with any tool. I tagged everything, and those cleanup steps are in our FAQs (and prior topics!). Looks good to me!

Shared history (click on it to view, and import if you want to!) → [https://usegalaxy.org/u/jen-galaxyproject/h/lactuca-sativa](https://usegalaxy.org/u/jen-galaxyproject/h/lactuca-sativa)

You can add the other files if you want to, but these two are your baseline.

Hope this helps! 🚀

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**Author:** ![Kelvin](https://avatars.discourse-cdn.com/v4/letter/k/7ba0ec/32.png) [@Kelvin](https://help.galaxyproject.org/u/Kelvin)\
**Post date:** [October 7, 2024, 5:20pm UTC](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608/3 "2024-10-07T17:20:58Z")

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Hello Jennifer,

Thank you so much. I appreciate it.