Question: Downloading GFF files from NCBI
gravatar for cjain
2.0 years ago by
cjain10 wrote:


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.


Chaitanya Jain

rna-seq • 3.5k views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by cjain10
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Refseq annotation files are available for many genomes from NCBI. See:

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 2.0 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour