Question

Downloading set of fasta sequences based on gene id

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4.9 years ago

shome ▴ 10

HI all, I have set of 21000 gene ids for tax id : 8479,for which I need to download fasta sequences from NCBI. How to do it using the command line terminal?

gene sequence geneid fasta • 2.7k views

ADD COMMENT • link updated 4.9 years ago by vkkodali_ncbi ★ 3.7k • written 4.9 years ago by shome ▴ 10

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What have you tried so far?

this question has likely been asked several times already ....

ADD REPLY • link 4.9 years ago by lieven.sterck 15k

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I have tried using Biomart and Batch entrez,but it didnt work well..

ADD REPLY • link 4.9 years ago by shome ▴ 10

score 0 · Answer 1 · 2019-05-28

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4.9 years ago

Emily 23k

BioMart.

ADD COMMENT • link 4.9 years ago by Emily 23k

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The species I am interested in is not in Biomart

ADD REPLY • link 4.9 years ago by shome ▴ 10

score 0 · Answer 2 · 2019-05-28

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4.9 years ago

vkkodali_ncbi ★ 3.7k

Use Entrez Direct. See: How do I set filter for NCBI esearch to get fasta for Genes only?

ADD COMMENT • link 4.9 years ago by vkkodali_ncbi ★ 3.7k