Folks, I wanted to scan the 2kb upstream of a list of human gene isoforms for TFBS using fuzznuc. I was able to "Get Data"> "UCSC Main" > "As sequence" and get my sequences "EMBOSS" > fuzznuc ran fine, and output the hits
HOWEVER, fuzznuc lost the genomic position information that UCSC has put after a space in the sequence headers of the FASTA file. It only provided offsets within the fasta. http://main.g2.bx.psu.edu/u/curtish-uab/h/ucsc-fuzznuc-ucsc-broken Thus, when I converted the fuzznuc output back to a BED file and tried to visualize the hits in UCSC browser, it failed with "invalid BED File". I tried fuzznuc with output: seqtable, feattable and gff3, but in all cases the genomic position was missing, and being a bit of Galaxy novice, I couldn't figure out how to get the output back to UCSC to visualize the hits. Can anyone tell me how to link up these tools correctly, or share a history with some other tool set that accomplishes this goal? Regards, Curtis Research Associate Center for Clinical and Translational Science University of Alabama at Birmingham ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
