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Old 09-17-2009, 12:04 AM   #1
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Default ChIP-seq Newbie

Hi,

I've recently been hired to work as a postdoc on ChIP-seq. It's a new technique for me, and the future supervisor has recommended a couple of papers to read up on it.

Could any ChIP-seq researchers kindly offer some pointers? I'd like to be as prepared as possible before starting the job. Are there any highly recommended papers for this area? Any popular software (and sample datasets) for ChIP-seq I could perhaps practice with? I noticed R / Bioconductor has some ChIP-seq functions; is this worth learning?

Would appreciate any tips/advice.. thanks

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Old 11-03-2011, 06:56 PM   #2
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Well, nobody replied to this at the time, but I just found it, two years later =)

The answer is yes, learn R/Bioconductor. Also learn Python as its faster for a lot of things. Also Linux is generally better as a lot of the good command line tools either don't work in windows or involve a lot of bother in getting them to work. One option is a virtual machine, though RAM/performance is something to consider.

Linux has things like RPy2 which allows R commands to be run within Python scripts. The way I like to do it though is to use separate R scripts which receive command line arguments (e.g. csv files produced by Python) to plot figures, etc. That works in windows too.

Finally, there is a bioinformatics website called Galaxy and another called Cistrome. Very good for starting out.
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