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Endogenous epitope messing with my alignment

Hi,

I have a question regarding some strange ChIPseq reads that I get. I endogenously tagged a gene with mCherry and FLAG ( 900bp total starting after ATG codon) and then wanted to see changes in chromatin modifications at this gene promoter (depending on the presence of different factors). I just got the ChIPseq results and I got a strong pick of reads at this location, even in my input (and nowhere else for my input). So, I am guessing that my tag is messing with the alignment... Any idea on how to solve this problem ?

Thank you !

chip-seq
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written by delphine.albrecht • delphine.albrecht

Can you show an example? Also, when you say "900bp total starting after ATG codon" are you really meaning to say that you put this on the N- rather than C- terminal? I half expect you basically truncated the gene and caused it to over-express. Am I correct in understanding that you're specifically interested in chromatin alterations around the gene you fused with mCherry and FLAG or is that a misunderstanding?

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written by Devon Ryan Devon Ryan

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