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Question: Uploading NCBI Genome
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gravatar for hackel.taylor
9 months ago by
hackel.taylor • 10
hackel.taylor • 10 wrote:

HI all,

I am having difficulty uploading a complete genome in fasta format. I have located the genome I would like to analyze on NCBI and have generated a webpage with the sequence in fasta format. However, when I upload the url https://www.ncbi.nlm.nih.gov/nuccore/NC_002951.2?report=fasta the database does not accept the url due to "innappropriate html". Also how can I download this fasta to my computer? When I tried to do so using NCBI as a Windows user I had to download Database Docs which puts the sequence in a binary format not accepted by most analytical tools. Thank you,

Taylor
upload download ncbi ftp fasta • 401 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by hackel.taylor • 10
1
gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are two steps when obtaining fasta data from this source:

  1. Download fasta genome sequence from NCBI using the "Send to" function. These graphics show the correct settings. More help is at their website. https://imgur.com/a/spkS8

  2. Then upload the fasta file to Galaxy using FTP: https://galaxyproject.org/ftp-upload/

And then there is a final QA step to ensure proper formatting for any fasta dataset. Usually, all you need to do is run the NormalizeFasta tool. How to: https://galaxyproject.org/learn/custom-genomes/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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