Question: Questions about addition of reference genome in Bowtie2
gravatar for garaman99
2.2 years ago by
garaman990 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?



ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson24k • written 2.2 years ago by garaman990
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson24k wrote:


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

How to:


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 COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson24k
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