Hi!
I am facing a very unique problem, I have a list of regions (in a bed file) and using GREAT and HOMER I annotated these regions to the near by genes. The problem is I do not get genes for few regions in a window of 500 base pairs ( that is fine, if the gene is not present), when I look up for these regions in UCSC browser I do find these regions present over a UCSC and RefSeq gene.
As an example, following are the regions
chr1 9747627 9748127 for this region PIK3CD can be seen in UCSC
chr1 6659871 6660371 for this region KLHL21
I have nearly 300 regions like this.
I am using hg19
Have you ever encountered such a problem? If yes how you have solved it? If no, what will be your approach?
Thank you,
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Dataminer
1 answer
Are you annotating using same genome build, with every new build the co-ordinates are shifted, might be a reason. (hg18 vs hg19)
I would download the list of genes from UCSC (refseq genes) and manually intersect them, the thing you are saying should not happen, might a small parameter problem.
Can you show your homer command used for annotation
Yeah, its fine, I just tested my annotation with homer, results are little different. Like it just annotated in summary, that 68 peaks are in promoters but I am positive for >300 peaks. Good idea to ask the author or you can manually look into the python code, how its happening.
Yes, thats what I said, by that you will be sure, what you are doing !!
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I just figured its hg19, please update in post for other people