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Question: GTF/GFF file generation
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gravatar for dzz0008
2.5 years ago by
dzz0008 • 0
dzz0008 • 0 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!

Dong
rna-seq • 832 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by dzz0008 • 0
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

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

Dongdong

ADD REPLY • link written 2.5 years ago by dzz0008 • 0
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