Help with PeakAnnotator

[Eagle_Eye]

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" (http://www.filedropper.com/peaks) and annotation file (should be chrom, start end-sorted BED) is "annotation.bed" (http://www.filedropper.com/annotation)

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

Any suggestions/help for troubleshooting?
Thanks

[heikomuller]

You may try the AnnotateGenomicRegions tool (http://bioserver.iit.ieo.eu/Annotate...ons/index.html). It does the sorting of your input regions internally.

[apredeus]

Any suggestions/help for troubleshooting?
Thanks

Hi! I realize it might be a bit late but I found this problem to be EXTREMELY annoying, so I spend quite some time and figured it out. I think it's worth posting it here to save people some frustration. The sorting that works is the following Unix sort:

sort -k1,1 -k2,2n -k3,3n file.bed > file.sorted.bed

You should sort both called peaks file and refrence annotation (RefSeq etc). Voila