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Old 08-24-2012, 08:03 AM   #2
Junior Member
Location: Paris, France

Join Date: Aug 2012
Posts: 2
Default PeakAnnotator PROBLEM

I am trying to annotate peak regions using PeakAnalyzer. I have problems with PeakAnnotator and I get this error message when I try to use the NDG function:

"Files must be sorted by chromosomes,start position, end position"

I tried several times to sort (using either excel or sortBED, still same error message)

I am attaching the files I am currently using: Peak file is "peaks.txt" ( and annotation file (should be chrom, start end-sorted BED) is "annotation.bed" (

Command line used:
> ./PeakAnnotator NDG peaks.txt annotation.bed output

Any suggestions for troubleshooting?
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