Question: Re: Ucsc->Emboss/Fuzznuc->Ucsc Workflow?
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
United States
Jennifer Hillman Jackson23k 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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ADD COMMENTlink modified 6.5 years ago by Robert Curtis Hendrickson130 • written 6.6 years ago by Jennifer Hillman Jackson23k
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gravatar for Robert Curtis Hendrickson
6.5 years ago by
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
ADD COMMENTlink written 6.5 years ago by Robert Curtis Hendrickson130
Hi Curtis, Two more steps were needed, I ran them in this history: http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/re-galaxy-user-ucsc- embossfuzznuc-ucsc-workflow-63 1 - removed the first column ("hg19") from dataset #38, using the "Text Manipulation -> Cut" tool 2 - in the resulting dataset #40, I used the pencil icon to change the file type to be "BED" and the metadata (column assignments) for a BED6 file were assigned After this, the UCSC link comes up (click on it to view there). Great job! If you want to, please consider publishing the Workflow along with a Page that describes the processing. Others using the fuzznuc tool would likely appreciate the help. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
ADD REPLYlink written 6.5 years ago by Jennifer Hillman Jackson23k
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gravatar for Robert Curtis Hendrickson
6.5 years ago by
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
ADD COMMENTlink written 6.5 years ago by Robert Curtis Hendrickson130
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