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PostPosted: Mon Oct 14, 2013 4:00 pm 
Your documentation says the first three columns are all that's required for GREAT however, my bed files has a fifth column containing a score (it's for the peak that is represented by each bed element). GREAT choked on this and said:

"Error details:
Line 1: The fifth field (score) must be an integer (not 64.10). Input data: 'chr1 815035 815904 MACS_peak_1 64.10'"

So it seems like GREAT doesn't just ignore data past column three. I wrote a program to round the scores and was able to proceed with the analysis but I'm wondering is there going to be a function associated with such scores in the future?
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PostPosted: Tue Oct 15, 2013 6:55 pm 
Site Admin
Thank you for your comment. We do not have plans to incorporate peak scores into our next major update, but would be open to suggestions for how this might be useful to our User community.

The GREAT team
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PostPosted: Fri Oct 18, 2013 5:32 pm 
Maybe the peak scores could be used as a ranking criteria. If peak A has a score that is 5X that of peak B then presumably the site of occupancy for peak B is more biologically relevant that peak A's site. Therefore the genes proximal to peak B might be more likely influenced by that greater genomic occupancy than for peak A.

I know I could always just append the scores onto the peaks later (in the region table). It's just a thought.

My initial query was mostly to alert you that columns past the third one can prevent GREAT from running. Thus columns beyond three are important for getting the program to run, just not for the output.
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