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Question: Add a reference genome
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gravatar for lidong460
21 months ago by
lidong460 • 0
lidong460 • 0 wrote:

Dear Mr./Ms., I just want to use HISAT in RNA-Seq, and I want to use Pseudomonas aeruginosa PAO1 as a reference genome, while it is not in the reference genome list. Can we add it in the reference genome list? I think we can get the whole genome of this bacterial strain from this link https://www.ncbi.nlm.nih.gov/nuccore/AE004091.2 Thank you very much!

Dong
rna-seq • 578 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by lidong460 • 0
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use this genome in fasta format in Galaxy as a Custom Reference Genome/Build. Run the tool NormalizeFasta as the first step after uploading to ensure proper formatting and to reduce problems that can occur with toosl when the fasta format is not standardized. This is how: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team
ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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