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?
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?