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Question: Downloading GFF files from NCBI
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gravatar for cjain
2.0 years ago by
cjain • 10
cjain • 10 wrote:

Hi:

Can someone help me figure out how to import a genome from the NCBI website into Galaxy in a GFF (or GTF) format? I would like to use HTSeq to quantify our RNA-seq reads onto the downloaded genome.

Thanks,

Chaitanya Jain
rna-seq • 3.5k views
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modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.0 years ago by cjain • 10
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gravatar for Jennifer Hillman Jackson
2.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Refseq annotation files are available for many genomes from NCBI. See: https://www.ncbi.nlm.nih.gov/refseq/

There are other sources depending on the organism/genome build version. Try UCSC, Ensembl, and the like. Before using with tools, make sure that the reference genome that the annotation is based on is an exact match for the reference genome in use. This includes ensuring that the chromosome identifiers are in the same format.

Best, Jen, Galaxy team
ADD COMMENT • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k
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