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Questions › Category: ChIP-Seq Data Analysis
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Should we always use histone markers just to see if our sequencing is working for our samples?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1357 views1 answers0 votes
What do you think about ChIP-seq with proteins that are highly mobile in nature? Why is there less data published about using them?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1175 views1 answers0 votes
I had great results with ChIP-qPCR, but when I did ChIP-seq only a few reactions came up with decent peaks. What could be the reason?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1233 views1 answers0 votes
Comparing to outside sources of data: What is a good website to check for transcription factor binding motifs and how they regulate expression?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1213 views1 answers0 votes
Comparing to outside sources of data: Do you have recommendations for frameworks or programs for integrating ChIP-seq and RNA-seq or microarray data?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1129 views1 answers0 votes
Library/ChIP preparation: What are nanobodies? Can they be used for ChIP-Seq?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1277 views1 answers0 votes
Replicates: Can you talk a little bit about IDR? Is IDR something you must do for transcription factor ChiP-seq or is it optional?> What about with histone marks? Does IDR work with MACS2 outputs?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1739 views1 answers0 votes
Replicates: If my replicates are highly reproducible, is it valid to merge my replicates before finding peaks?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1739 views1 answers0 votes
Peak calling and analyses: What do you think about ChIPseeker for annotation?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1411 views1 answers0 votes
Peak calling and analyses: When I call peaks with MACS2, can I use one ChIP (antibody1) as the control for a second ChIP antibody? Can I detect differences between the two proteins that way?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1810 views1 answers0 votes
Peak calling and analyses: If the control is input, which method peak calling do you prefer?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1236 views1 answers0 votes
Peak calling and analyses: What peak caller is good for broad peaks?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1365 views1 answers0 votes
Pipelines and QC:What package do you use to perform a partial duplicate removal?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1187 views1 answers0 votes
Pipelines and QC: Does the mouse genome have a blacklist file?
Answeredstonelakeak@nih.gov answered 2 years ago • 
1243 views1 answers0 votes
Pipelines and QC: When and how do you remove blacklisted regions? What program do you use?
Answeredstonelakeak@nih.gov answered 2 years ago • 
2208 views1 answers0 votes
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