toolannotatePeaks.pl takes a BED file and a genome file. Are you providing the proper genome file/name ? Check if the chromosome names are same ? Like 'Chr1' or '1' in both Genome and BED file ? Post the exact command used and first few lines of BED file.

Hi All,

I'm facing similar issue from HOMER tool, reported by gpdus67. I have checked my peaks file and the genome file both have 'chr1' only. Still I always end up getting blank values in Annotated peak file. Is there anything to do with makeTagDirectory output? Command used:

./annotatePeaks.pl path-to-dir/peaks.txt hg18 > annotatedpeaks.txt

What am I doing wrong?

Peaks file also contains a lot of commented information in the beginning. Does it needs to be removed? Few lines from my peaks file:

#PeakID chr     start   end     strand  Normalized Tag Count    focus ratio     findPeaks Score Fold Change vs Local    p-value vs Local        Clonal Fold Change
chr1-1  chr1    91625448        91625674        +       258.5   0.584   378.000000      84.31   0.00e+00        0.49
chr1-2  chr1    154452940       154453166       +       255.1   0.597   372.000000      54.33   0.00e+00        0.49
chr1-4  chr1    121186277       121186503       +       214.0   0.561   314.000000      13.15   1.48e-225       0.54

I am tired of getting empty annotated peak file. Please help.

Thanks in advance.

you can try ChIPseeker.

Hi gpdus67 and Rituriya, I'm not sure if this will help, but I had the same issue too--- I ended up needing to convert my .txt peak file from a Macs-based .txt file into an acceptable .txt file that annotate.pl could handle. So, in Homer, I did:

changeNewLine.pl path/peakfile.txt

I did this for all of my peak files... then it was able to annotate my stuff. Hope this helps! ~Diana