Question: How do I get reference genome?
gravatar for andonai
2.9 years ago by
andonai0 wrote:

There is no reference genome for leishmania in Bowtie2 tool - map reads against reference genome. How do I get?

galaxy • 1.8k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by andonai0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Add the genome to your account as a Custom Reference Genome.

How to:

Extra details for successfully using a custom genome are in this tutorial: Fasta Format, Custom Genomes, and GATK Chromosome ordering

While the tutorial focuses on a specific human genome example, the general rules about verifying sequence identifiers and the other ways to avoid data mismatch issues will apply to all genomes. That information is covered in the wiki, but sometimes reading about a specific example can be helpful.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
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