I want to use annotatePeaks.pl from HOMER to annotate my ChIP-seq peaks. It works but the column for
gene name.etc is missing.
Here is the result:
PeakID (cmd=sample1_uniq_peaks.bed /work/finger3/MotifHOMER/data/genomes/mm9/) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type 37 chr1 49627683 49629512 0 0 NA Intergenic NA -1355770 NM_019790
I check the manual of HOMER.
The data I use is mm9 and mm9.tss is included in the directory.
Is there anyway to annotate the peaks with gene symbol/name since my gene expression file is annotated with gene name like p53.