Question: homer-annotation of the minus strand genes
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gravatar for c2c12
14 months ago by
c2c120
NY/USA
c2c120 wrote:

Hi, I'm trying to use Homer to annotate peaks from the analysis in the Diffbind . I noticed recently that even when I'm assigning peaks as 0 or 1 (I don't have that information from the Diffbind) or forcing -strand plus or -strand minus, annotatePeaks.pl ignores the genes on the minus strand . For example, I have a peak with coordinates chr6 64295326 64295728 (hg38) annotated as PHF3 by Homer, but in the UCSC genome browser it falls in the middle of EYS gene on the opposite strand, and PHF3 is far far away 649001 bp from it's promoter. I checked, that any of the genes annotated by Homer doesn't fall on the minus strand. I suppose that it's choosing the nearest tss but not taking into the account the length of the gene. How can I fix it to annotate all genes? I'd be grateful for help

the command I'm using for annotating both strands: annotatePeaks.pl MSC_Diffbind_both.bed hg38 > MSC_Diffbind_homer_anno_both.txt -go MSC_Diffbind_homer_GO_both -annStats MSC_Diffbind_homer_summary_both.txt -nmotifs -mdist -CpG -mbed MSC_Diffbind_motifs_both.bed -strand both

view from the genome browser

annotation strand homer 5hmc • 519 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by c2c120
1

Hi, I have the same problem! Nobody know how to fix?

ADD REPLYlink written 11 months ago by edoardo.abeni10
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