Question: Downloading GFF files from NCBI
0
gravatar for cjain
21 months ago by
cjain0
cjain0 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 • 2.3k views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by cjain0
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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