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PostPosted: Tue Oct 08, 2013 10:40 am 
Hi,
I somehow couldn't find it in the nicely detailed descriptions and help topics:

I want to find the list of genes associated with each of my original loci; e.g. if I had the regions:
chr1 4482767 4482770
chr1 4775858 4775907
chr1 4792828 4792840
chr1 4847633 4847669
chr1 5127270 5127316
chr1 5218163 5218179
chr1 7079100 7079110

I got for this set an annotation, I was hoping to know for EACH loci, what genes where associated with it by the algorithm. I now get just annotations of "unnamed". Should I add a column to my original BED file with an annotation for each loci?

unnamed Sox17 (+69535)
unnamed Sox17 (+3691)
unnamed Sox17 (+2004)
unnamed Sox17 (-47787)
‚Äč
Thanks much!
Alon
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PostPosted: Tue Oct 15, 2013 7:02 pm 
Site Admin
Hi Alon,

Yes the best way to do this currently is to add a unique identifier to each loci as a 4th row in the input bed file. This will replace, for example:

unnamed Sox17 (+69535)
unnamed Sox17 (+3691)
unnamed Sox17 (+2004)
unnamed Sox17 (-47787)

with

id1 Sox17 (+69535)
id2 Sox17 (+3691)
id3 Sox17 (+2004)
id4 Sox17 (-47787)

Thanks,
The GREAT Team
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