Question: GTF/GFF file generation
gravatar for dzz0008
2.5 years ago by
dzz00080 wrote:

Hi galaxy team,

I want ask how can I generate the gene annotation GTF/ GFF files? My studied organism is Pompano fish, not the model organisms like Drosophila malanogaster that can be download directly from UCSC. But I really need the that file to do Gene-based read counting with HTseq-count.

Thanks so much!


rna-seq • 832 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by dzz00080
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Creating an annotation file is non-trivial. It is best to locate a GTF file of annotation based on the same reference genome as used for mapping. I don't know of a source, but places to check are Biomart, Ensembl, etc.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k

Thanks Jen. So if that organism does not have reference genome, we could not locate the GTF file?


ADD REPLYlink written 2.5 years ago by dzz00080
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