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Question: Questions about addition of reference genome in Bowtie2
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gravatar for garaman99
2.8 years ago by
garaman99 • 0
garaman99 • 0 wrote:

 

Now I'm going to analyze my ChIP-seq data with Galaxy, but there is not the species I want on the list.

I performed the ChIP-seq using Cryptococcus neoformans var. grubii H99S strain.

So, could you add C. neoformans on the reference genome?

 

 
reference genome addition bowtie2 • 744 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by garaman99 • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For smaller genomes, using a Custom Reference Genome is the best way to use these quickly with tools.

How to: https://wiki.galaxyproject.org/Support#Custom_reference_genome

 

Extra help, focused on another genome, but explains in more detail the importance of using correct and simple fasta format from the start of an analysis project: Fasta Format, Custom Genomes, and GATK Chromosome ordering

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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