Question: process bed/bedGraph files with the same coordinates for all the samples
gravatar for Kath
5 months ago by
Kath0 wrote:

I have large number of ChIPSeq samples and would like to generate bed/bedGraph files all with the same genomic coordinates. would any one help to provide any advice on this? Thank you in advance!

chipseq • 120 views
ADD COMMENTlink written 5 months ago by Kath0

You need to more clearly explain what you want. If I were to interpret your question, I would think you want like a gazillion bed files, all with the same thing in each, which obviously makes no sense.

ADD REPLYlink written 5 months ago by James W. MacDonald51k

James, thank you and this is the first time I get into this question and was wondering as well. I am using ChIPSeqSpike package and inputsubtraction step gave the errors, I was told to provide all the bed/bedGraph files in the same coordinates. Not sure how to proceed with it so I posted here for more advice.

Meantime, do you have any advice on normalization of ChIPSeq data with exogenous genome DNA spike in? Thank you in advance!

ADD REPLYlink modified 5 months ago • written 5 months ago by Kath0

OK. It looks like you have contacted the maintainer of that package with a question, and he told you to do something? If so, you might get clarification from him, rather than here, as we have no idea what he is asking for, but he (one would assume) does. I would also assume that he could provide you with some code to help you get what he wants?

I don't have any advice for you concerning normalization. This site is primarily intended as a place that people can ask technical questions about how to get the software to do what they want it to do, with the implicit assumption that the person asking has the required statistical knowledge, but may not have the required technical knowledge for a given package.

What you are asking is a statistical question, which is almost always more difficult than a technical question, and would require me (or anybody else) to know more about your experiment, the goals, etc. This isn't a straightforward question, and there is usually not one 'right' answer. As an example, the csaw package has a workflow that goes through all the things you could do to normalize your data, but leaves it up to you to decide what's best.

As the analyst you have taken on the responsibility of knowing all the ways you could normalize your data, choosing one, and being able to defend your choice. If you can't do all three of those things, you should probably get some local help. Analyzing ChIP-Seq data is a non-trivial task

ADD REPLYlink written 5 months ago by James W. MacDonald51k

Thanks for your comments

ADD REPLYlink written 5 months ago by Kath0

In addition to James' comments, the csaw user's guide also has some comments about spike-in normalization (Section 4.5 in ).

ADD REPLYlink written 5 months ago by Aaron Lun25k
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