Question: splice junction file for human(hg19)
gravatar for Govardhan Anande
3.5 years ago by
Govardhan Anande130 wrote:

Where can I get splice junction annotation file for human(hg19), in order to run tophat with --raw-juncs.

Thanks in advance

ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 3.5 years ago by Govardhan Anande130

In tophat manual, when "you supply your own transcript annotation data", you should use "--raw-juncs." option.

Normaly(i.e. when dont have our OWN transcript annotation data including splice junction interval), GFF or GTF annotation file includes splice junction informatin.

ADD REPLYlink written 3.3 years ago by cfarmeri150
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