[BioC] Chip-seq quality control

[Ivan Gregoretti]

Hello Lucia,

A proper response to your post would take a lecture rather than an
email. I can't do that but I can bullet the main points. I think that
it will help you if you are indeed a newcomer to ChIP-seq.

1) Expect 10 million reads per sample for a genome the size of human.

2) Stick to SAM/BAM formats so that you can use well known, publicly
available tools. Your best friend is called Picard.

3) Remove duplicates. Again, Picard is your best friend.

4) Create WIG files for all samples, treatments and controls so that
you can display them simultaneously on any genome browser.

5) Find peaks with a well documented peak finder.

6) Compute enrichment for all treatments relative to their controls.


So, points 4 and 6 are your quality controls at this stage. Once you
know what a good immunoprecipitation looks like compared to a bad one,
you can start diving into the details. You can invent your own quality
indicators. For instance, I compute the proportion of tags inside the
1000 strongest peaks. I do that for BOTH treatment and controls.

In my workflow, Bioconductor does not get involved until I reach point 6.

Happy ChIPing.

Ivan





On Mon, Oct 3, 2011 at 5:17 PM, Lucia Peixoto <luciap at iscb.org> wrote:
> Hi,
> I am new to Chip-seq, my experiment's sequencing has finished, and the read
> alignment is currently running
> The experiment  was done for histone acetylation, and I have two types of
> controls: input DNA and unmodified histone.
> I have two conditions and 6 biological replicates of each condition
> I wanted some advice on how to perform basic quality control on Chip-seq
> data using Bioconductor
> and also some ideas of which kinds of biases people usually observe and I
> should keep my eyes open for
> any advice will be greatly appreciated!
> thanks
>
> Lucia
>
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