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.

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? 


Research Associate
Center for Clinical and Translational Science
University of Alabama at Birmingham

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