How to add and use a custom reference genome

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Question: How to add and use a custom reference genome

6 months ago by

wy412 • 0

wy412 • 0 wrote:

Dear Sir or Madam,

May I know how to add some other genome information for custemerized analysis on some other plant genome reference, such as Sesamum indicum. There is genome information in NCBI database. How to upload to Galaxy and do RNA-seq analysis?

Hope you can teach me to solve this problem.

Thanks and best regards,

Your sincerely, Yi

fasta build genome custom rna-seq • 266 views

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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by wy412 • 0

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Download the fasta version of the genome and upload it to Galaxy. Then use it as a Custom reference genome with tools. Getting the associated reference annotation GTF would also be a good idea, as it is commonly utilized or required by RNA-seq tools.

Use FTP to load any data over 2 GB in size up to Galaxy.

Support FAQs: https://galaxyproject.org/support/

Loading Data https://galaxyproject.org/support/loading-data/
Common datatypes explained https://galaxyproject.org/learn/datatypes/
Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/

Galaxy Tutorials, including those for RNA-seq: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team

ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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