Question: Uploading NCBI Genome
gravatar for hackel.taylor
9 months ago by
hackel.taylor10 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 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,


upload download ncbi ftp fasta • 401 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 9 months ago by hackel.taylor10
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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.

  2. Then upload the fasta file to Galaxy using FTP:

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:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
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