Having provided a name (field 4) in a UCSC bed file ( 
http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1 ) and sought a RefSeq 
name using the UCSC Table Browser ( http://www.genome.ucsc.edu/cgi-bin/hgTables 
), I would now like to recover which line of the bed file delivered which line 
of the output fileā€¦ However, I am told I need Galaxy to provide a workflow to 
do this.  Can anyone explain how?  eg, one line of my bedfile looks like:
chr2    2723752 2723777 seqid6354405    0       -
and one line of my intersected table browser output looks like:
chr1    176432306       176811970       NM_020318       0       +       
176525458       176811590       0       23      

Clearly the first line of my bed doesn't correspond to the first line of my 
intersection output, but as my bed is long, what reference can I use to 
unambiguously identify which line of output the first line of my intersection 
corresponds to?  How do I do this in Galaxy?

PS - I tried this workflow earlier today without success, aiming to achieve a 
similar objective: 

PPS- I also note similar issues were raised in this discussion, with Galaxy 
promoted as the solution, but with no real details about how to achieve the 
desired results:

Bert Gold, Ph.D., FACMG
Staff Scientist
Frederick, MD 21702
VOICE: 301-846-5098
EMAIL: go...@mail.nih.gov
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