Hello.
I was looking at the correlation of signal intensities between two biological replicates (ChIP-Seq) and I got a strange plot. I was wondering if anyone has seen something like this before, or if anyone has any ideas of why this is happening.
I counted the number of reads in 1kb windows across the whole genome, and plotted replicate 1 Vs. replicate 2. In the image it shows the raw signal and the normalized "Reads per million" signal.
There seems to be some kind of an "offset" between two trend lines in the plot:
I have looked at the GC content, and position relative to genes (exons, introns, TSS, TTS) of the windows that are in the two different "offsets", and nothing came out as significantly different.
Any ideas would be very much appreciated!
Many thanks!
ines
I was looking at the correlation of signal intensities between two biological replicates (ChIP-Seq) and I got a strange plot. I was wondering if anyone has seen something like this before, or if anyone has any ideas of why this is happening.
I counted the number of reads in 1kb windows across the whole genome, and plotted replicate 1 Vs. replicate 2. In the image it shows the raw signal and the normalized "Reads per million" signal.
There seems to be some kind of an "offset" between two trend lines in the plot:
I have looked at the GC content, and position relative to genes (exons, introns, TSS, TTS) of the windows that are in the two different "offsets", and nothing came out as significantly different.
Any ideas would be very much appreciated!
Many thanks!
ines
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