Hi All,
I am using homer annotatePeaks.pl (version 4.11) by providing the bed file. Surprisingly, in the output file all peaks start position is increasing by +1, while the end remains same as in the input bed file. I read through homer annotatePeaks.pl help page but not finding any reason specific to this context.
"Command used":
annotatePeaks.pl Tumor_vs_Normal_peak_annotation_input_file.bed hg38 -annStats Tumor_vs_Normal_peaks_stats.txt -CpG -go GO_analysis_results -genomeOntology genome_ontology_results >Tumor_vs_Normal_homer_annotation_output.txt"
Input file: tail Tumor_vs_Normal_peak_annotation_input_file.bed
chrM 10857 11082 peak_677899
chrM 13955 14612 peak_677900
As we seen in output file chr start site is. 13955 and 10857.
"Output file (only first few columns are shown):" tail Tumor_vs_Normal_homer_annotation_output.txt
peak_677899 chrM 10858 11082 + 0 NA Intergenic ncRNA 0.013393 0.417778
peak_677900 chrM 13956 14612 + 0 NA Intergenic ncRNA 0.013720 0.429224
As we seen in output file chr start site is. 13956 and 10858.
I do understand that annotation tools can be 0 and 1-based. But is there a way to retain peaks regions similar to input bed file? or I need to subtract 1 from all entries in that column?
Thanks
Rakesh
