I am using annotatepeaks.pl function from HOMER to annotate my peaks to the nearest refseq gene. If you have used the tool you will notice it generates 10 columns. I am interested (or the columns which make me interested) are distance to TSS, nearest promoter id, nearest RefSeq ID, and gene name.
Problem: At times the peak is annotated to the nearest promoter id with some distance to TSS, while the column with nearest RefSeq ID and gene name goes blank.
Since I am interested in finding the nearest gene to my peak hence I am interested in nearest Refseq Id and in gene name but if these two columns go blank and distance to nearest TSS does not, then I think I am in bit of trouble (or not)? or is it completely normal that in nearest Promoter Id we can have some id while nearest Refseq Id goes blank and gene name?
I am completely confused.
Thank you please try to answer.