Question: (Closed) Measure fold change of super enhancer regions
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gravatar for aropri
9 weeks ago by
aropri70
aropri70 wrote:

This question was closed but I am asking a different way to discover lost/acquired super enhancers in normal vs. breast cancer cells. Please let do not close this question. So briefly, I did ChIP seq using H3K27ac antibody to quantify super enhancer regions in normal vs breast cancer cells. I ran ROSE algorithm on normal mammary epithelial cells and breast cancer cells to get a list of super enhancer regions in each cell line. I have a list of super enhancer regions for both and I want to compare super enhancers between the two outputs I got. I want to compare the signal of the super enhancer regions that were classified by ROSE in normal and breast cancer cells and see calculate fold change of those regions to see if they are increasing or decreasing in intensity. I have a bed files of super enhancer regions for normal cells (MCF10A) and same for breast cancer cells (MCF10A-CA1). I know what I have to do. Briefly, collapse A.SE.bed and B.SE.bed into AllSEs.bed using bedtools merge. Quantify coverage of All SEs.bed using A.bam and B.bam and bedtools intersect. Normalize the read coverage to the sequencing depth, and calculate the fold-change between them. The problem I was having is how can I collapse or merge two or three bed files into one file that will contain all the super enhancer regions classified and quantify coverage? Any help is appreciated. Thank you so much!

chip-seq • 144 views
ADD COMMENTlink written 9 weeks ago by aropri70

Hello aropri!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 9 weeks ago by ATpoint44k

aropri, I did not close the other one for my personal joy ( this one here Compare Super Enhancers in normal vs breast cancer cells ). The topic is identical to your original question. Please follow up on the original one, which means please add comments or edit it to explain what you need to solve your issue. Stop opening identical questions. You can edit the first question using the edit button. One user already provided an answer there, you can comment on it to ask for more details. The idea of closing identical questions is to keep information focused in a single rather than multiple threads, please respect these very basic forum rules.

Original question: Compare Super Enhancers in normal vs breast cancer cells

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by ATpoint44k

Ok, I apologize for my misunderstanding.

ADD REPLYlink written 9 weeks ago by aropri70

No problem.

ADD REPLYlink written 9 weeks ago by ATpoint44k
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