How to annotate peaks without strand information
Hi there,
I'm sorry if this question has been asked before. I'm trying to assign gene names to specific coordinates using HOMER. I am able to run the script but I find that some incorrect gene names are assigned to some coordinates. I think it has to do with the strand. I have no strand information, but clearly these coordinates lie within a gene, but HOMER outputs the neighboring gene. I think because the coordinates are in the negative strand and HOMER assumes it should be the positive strand and so outputs the name of the neighboring gene that is in the positive strand. So the question. Is there a way to remove strand information? Thanks in advance
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Please add representative information such as a screenshot. Check if the TSS of the assigned gene is closer to the peak than the TSS of the overlapping gene.