User: Researcher
Researcher • 50
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... Hi [Kristin][1], I also have 5 samples from two conditions and struggling with the same concern you mentioned above. Did you get the answer to your question, will you mind sharing your experience with the problem?
Thanks in advance!
[1]: https://www.biostars.org/u/13153/ ...
written 4 weeks ago by
Researcher • 50
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... Hi [Jared][1] thank you for your reply.
I just left a same question [here][2] , please have a look.
I hope you meant the same?
I am really stuck with this and looking for a way out.
[1]: https://www.biostars.org/u/40195/
[2]: https://www.biostars.org/p/406421/ ...
written 5 weeks ago by
Researcher • 50
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... Hi [venu][1],
I am a bit lost and seeking your help.
Actually I have 10 bed files from 10 samples, each one has a different start and end coordinates based on their SEs. But I am confused about making a common bed file from all these together in order to generate the read count matrix.
Before usin ...
written 5 weeks ago by
Researcher • 50
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... Hi All,
I have 10 bed files generated by ROSE, each with distinct start-end cordinates for SuperEnhancers (SEs) from 10 different samples, 5 of them are from one condition and rest 5 are from other. In order to check the differential binding for these SEs between the two conditions, I have parsed th ...
written 5 weeks ago by
Researcher • 50
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... Hi [@Zhao03][1],
Did you figured out the answer you were looking for displaying the sample names as column names or row names?
Please share your experience.
Thanks
[1]: https://www.biostars.org/u/53239/ ...
written 5 weeks ago by
Researcher • 50
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... Hi [ATpoint][1], Thank you so much such a nice description. Can you please again explain which summit option have you just mentioned? Is it from MACS2 or DiffBind as both the tools have an option with the same name "summit" and I am not sure which one will be helpful for the cause.
Thanks again!
...
written 6 weeks ago by
Researcher • 50
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... Thank you all, for your helpful suggestions. I must say and appreciate it is really a nice platform for a newbie like me to get such valuable insights.
Best ...
written 6 weeks ago by
Researcher • 50
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6 follow
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... Hi All,
I want to use bed files having list of super-enhancers identified in each samples generated from ROSE and to check the their differential binding. Towards this I have few questions:
Can I use DiffBind for this?
Is it possible to use DiffBind to read bed files and looking at their respective ...
written 6 weeks ago by
Researcher • 50
• updated
6 weeks ago by
sim.j.baum • 50
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... Thanks [ATpoint][1] for your reply.
But I am wondering about the sites that have different start and end loci but are overlapping. How should I deal with that?
[1]: https://www.biostars.org/u/25721/ ...
written 9 weeks ago by
Researcher • 50
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... Hi All,
I have ranked my chip-seq peaks and calculated the probable super enhancers using ROSE for my samples from different subtypes of cancer. Now I want to perform unsupervised clustering based on enriched SE regions to see whether the samples from same cancer subtype cluster together or not.
Ca ...
written 9 weeks ago by
Researcher • 50
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