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

Jennifer, Thanks for your help so far. I've been trying to implement the approach you outlined. It seems to be taking a lot of steps. I think I'm now at the last step, where I convert my TAB format file into a BED and push it to USCS for viewing. But I don't see anything that will allow me to do that last conversion step. http://main.g2.bx.psu.edu/u/curtish-uab/h/fuzznuc Any advice would be appreciated. Curtis

Jen, Thanks for all your help. Here's the final Galaxy workflow for doing FUZZNUC on a BED file from UCSC Table Browser, then producing BED file that you can view in UCSC. http://main.g2.bx.psu.edu/u/curtish-uab/w/fuzznucucscbed I do not include the "Get Flank" operation in this base workflow, but include a note in the description. I have not (yet) had time to make the score in the final BED dependent on the quality of the match, when mis-matches are allowed, but I hope to come back and add that later. How does one handle versioning of published workflows? Do updated the existing one, or create another with a .v2 name? Also, I used several "Text Manipulation> Compute" steps - is there any way to compute more than 1 new column at a time? Regards, Curtis