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