Request for Custom Bowtie Tool Interface for Human Reference Genome Alignment

[Armana]

Hello Galaxy Team,

I am working on small RNA-seq analysis using Galaxy, and I need to perform an alignment using the Bowtie tool with a human reference genome and my small RNA samples. I have already uploaded my sample data (FASTQ files) and the human reference genome (GRCh38) to Galaxy. However, I require a custom interface for Bowtie that will allow me to easily upload the data and reference genome, and adjust the necessary parameters for alignment.

[jennaj]

Welcome @Armana

Yes! You can use Bowtie2 in Galaxy for this type of analysis.

Using Galaxy tool forms

We have a tutorial here that walks through some of the basic guidelines for working with a mapping tool. → Hands-on: Mapping / Mapping / Sequence analysis

The tutorial above uses a reference genome that is already indexed on the server, however you can use any reference genome that you want to! Just upload the genome fasta and use the reference genome From the History option instead. You will be selecting your fasta in a similar way that you will be selecting the input read datasets.

Sourcing Reference Data

We have some help for getting a reference genome, and the associated reference annotation, into your history! This prior topic is a good place to start.
~

@jennaj

Reference data is self-serve in Galaxy!

Custom Genomes with (optional) Custom Builds

You can use any genome assembly with tools! Load up the reference genome fasta and paired reference annotation GTF files into your history, select these on tool forms (using the option “Custom Genome from the history”), and tool specific indexes will be generated on demand.

If you later need a database key, you can create a Custom Build and assign that to your datasets, too!

More details here:

@jennaj

Please use the Custom Genome functions with tools. This will use reference data from your history. → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at

You can load the data from the data provider of your choice. This is a guide about how to get the data (genome + annotation) from NCBI. → FAQ: NCBI reference data

More examples can be found under the tag custom-genome

We hope this helps!

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Please give that a review and let us know if you have more questions or need help!

• Galaxy Training!
• Reference genomes at public Galaxy servers: GRCh38/hg38 example