Question: Re: Ucsc->Emboss/Fuzznuc->Ucsc Workflow?
7.3 years ago by
Jennifer Hillman Jackson ♦ 25k
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Curtis, The BED extraction data can be resolved in Galaxy. Pull out the whole gene and then modify the coordinates in Galaxy to be 10k upstream. To be clear - this coordinate data is going to be used to transform the coordinates in your current fuzznuc output that is transcript-based to be genome-based. The coordinates are not input for fuzznuc - the are used after fuzznuc is run on the fasta file, in order to covert the result coordinates only. This page in the UCSC wiki has a good description of how the UCSC coordinates are organized. http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms The output format for fuzznuc is documented in the tool's help - the last line on the tool form has a link. Hopefully this helps to clear up the suggested processing, Thanks, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
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