Hi:
I have a BED file with sites of a transcription factor binding sites (mm9).  I want to annotate these sites, typically located between intergenic regions, to a gene nearby.  I checked a publication (PMC3080774) and it lists some tools that can map and annotate. 
I tried using Chipseqanno. Initially it was straightforward till first two commands (https://bioconductor.org/packages/release/bioc/vignettes/ChIPpeakAnno/inst/doc/pipeline.html) and it went confusing. 

 

   

     bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno")
        gr1 <- toGRanges(bed, format="BED", header=FALSE) 
        ## one can also try import from rtracklayer
        gff <- system.file("extdata", "GFF_peaks.gff", package="ChIPpeakAnno")
        gr2 <- toGRanges(gff, format="GFF", header=FALSE, skip=3)
        ## must keep the class exactly same as gr1$score, i.e., numeric.
       gr2$score <- as.numeric(gr2$score) 
       ol <- findOverlapsOfPeaks(gr1, gr2)
        ## add metadata (mean of score) to the overlapping peaks

Authors did not explain why they are overlapping gr1 and gr2.  Before that authors say "## one can also try import from rtracklayer". also authors did not point out names for annotations MM8 or Hg19. 

My question to this forum is:
1. Given a bed file how can I map and annotate the peak regions to nearby genes. 
2. Can I define 1kb, 2kb range. (apparently chipseqanno uses granges and thus is possible- however lack of mm9 and proper reference to why findOverlaps between gr1 and gr2 makes it so confusing to deal with ranges). 
3. Are there any tools other than chipseqanno to achieve above two tasks. 

Thanks
Adrian

You can try using [annotatePeaks.pl][1] which is a simple perl script, a part of [HOMER][2] package. You basically need 3 files for running it:

 1. Peak bed file 
 2. reference genome fasta file 
 3. reference genome annotation (gtf/gff) file

And command goes like this:

perl annotatePeaks.pl sample_peak.bed Genome.fasta -gft genome.gft >homer_annotation.txt	

				


  [1]: http://homer.ucsd.edu/homer/ngs/annotation.html
  [2]: http://homer.ucsd.edu/homer/