Question: Noisy Histone ChIP Seq data
gravatar for VY
3.7 years ago by
VY120 wrote:



I got back some data in the format of aligned BAM files for three histone IPs I did on H3K27me3, H3K4me3 and H3K36me3.

After doing peak calling and processing bed files in IGB, when I generate Depth graphs I see that there is alot of noise, for examples my H3K27me3 gives spikes throughout the gene rather than a peak as you would expect. Also H3K36me3 for example has peaks in the middle of two random genes, which you wouldn't expect as its an elongation mark.

My question is, what are your suggestions to minimize the noise and at what stage?



histone chip-seq • 938 views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by VY120
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I am not sure what tool you are using to call peaks, but setting the stringency for peak calls seems to be what is needed. How to do this can vary by tool - but on each tool form is a link to the 3rd party documentation (or you can google it).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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