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Old 10-03-2011, 09:52 AM   #1
Mela
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Question ChIP-seq: time needed for data analysis?

Hi there!
I am a biologist and have never ever dealt with NGS and bioinformatics before...
My boss and I plan to do a genome-wide ChIP-seq experiment and a RNA-seq analysis (looking for genes that are regulated by a TF under different culture conditions).
I tried to find out how long the data analysis of these experiments will take, but couldn't find any answer. Can anyone give me a precise answer, maybe in weeks?

Thanks a lot,
Mela
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Old 10-03-2011, 10:00 AM   #2
kopi-o
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ChIP-seq analysis should typically go faster than RNA-seq analysis. But it all depends on what you want to do. A "cookie-cutter" ChIP-seq analysis can be done within a day by an experienced bioinformatician, but a more likely timeframe would be a couple of weeks. Again, it depends. You will probably want to combine your results with published data sets and that could take any amount of time.

Edit: Note that this only refers to the ChIP-seq part, since you specifically asked about it in the title. The analysis of the RNA-seq part will take at least as long and then you need to decide how to combine the information from your experiments, which will also take some time.

Last edited by kopi-o; 10-03-2011 at 10:05 AM.
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Old 10-03-2011, 12:09 PM   #3
Mela
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Thank you very much for your answer. so, it all depends on how detailed the data is analyzed?

My problem is that we want to apply for a grant for this project, and that we have to give a detailed time frame for the project. I have no idea what time is reasonable for the data analysis. Is there kind of a guideline how to calculate the time for data analysis for grant applications?
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Old 10-03-2011, 02:36 PM   #4
kopi-o
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I don't know if there are any guidelines, but I would put several months just to be on the safe side.
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Old 10-04-2011, 12:45 AM   #5
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It is impossible to predict how long such an analysis will take. Of course it depends on the experience of the bioinformatician. But even more it will depend on how well the question you ask is formulated and how well your experiment covers the question.
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