# Download and Extract Reads in BAM

**URL:** <https://help.galaxyproject.org/t/download-and-extract-reads-in-bam/13484>\
**Category:** Uncategorized\
**Tags:** troubleshooting, tool-help\
**Created:** [September 19, 2024, 6:12am UTC](https://help.galaxyproject.org/t/download-and-extract-reads-in-bam/13484 "2024-09-19T06:12:56Z")\
**Posts on this page:** 1\
**Showing post:** 2

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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 19, 2024, 5:14pm UTC](https://help.galaxyproject.org/t/download-and-extract-reads-in-bam/13484/2 "2024-09-19T17:14:29Z")

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Welcome, @Shailesh_Kumar_Dhuda

You can map against any reference genome in Galaxy. You’ll need to source the fasta, load it into a Galaxy history, then choose the “from the history” option on the tool form.

Please start here → [Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj](https://help.galaxyproject.org/t/custom-genome-custom-build-how-to-use-a-genome-that-is-not-natively-indexed-at-the-server-you-are-working-at/10082/2)

For loading the reference genome fasta, you can usually just copy/paste the file URL from a public source into the Upload tool. Or, locally browse and file on your computer and load the file that way.

- [Getting Data into Galaxy](https://help.galaxyproject.org/docs?topic=10868)

Then, for mapping in general, please see the tutorials here to start with.

- Using a reference genome index already on the server → [Hands-on: Mapping / Mapping / Sequence analysis](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html)
- Using a reference genome fasta from the history → [Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization / SARS-CoV-2 Viral Sample Alignment and Variant Visualization / Sequence analysis](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html)

If you haven’t used Galaxy before, we have some simple “first time” tutorials here, too.

- [Introduction to Galaxy Analyses / Tutorial List](https://training.galaxyproject.org/training-material/topics/introduction/)

If I misunderstood what you are trying to do, or you need detailed help, please explain a bit more please. 🙂

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