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Old 07-29-2013, 08:17 AM   #1
julieanadel
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Location: Bronx, NY

Join Date: Jul 2013
Posts: 1
Question D. Melanogaster ChIP

I recently tried to do a ChIP-like experiment on chromatin from drosophila S2 cells and found that a large portion of my ChIP reads, but also my input reads, aligned to repetitive elements. I have done this experiment in human cells before and not had this result. I wasn't sure if this was a hallmark of trying to do sequencing in Drosophila, or if it was just a problem with my particular assay.

Has anyone seen a problem like this before?

Is there anything I can change in my alignment (done using MACS), or in my analysis to avoid this?
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alignment problem, chip, drosophila, repetitive elements

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