User: Wet&DryImmunology
Wet&DryImmunology • 220
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- Japan
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- 2 years, 1 month ago
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Posts by Wet&DryImmunology
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... @Ryan, thank you for your suggestion. I guess (B) the off-specifies spike-in is the definitive solution. For (A) could you explain a little more? it did not seem to be obvious to me why normalized to non peak region would address the issue. I did some homework about "Diffbind", it seems to me that ...
written 2.1 years ago by
Wet&DryImmunology • 220
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... Hi, Hi, I was trying to investigate the changes of H3K27ac upon conditional KO of gene X.
After mapping and counting the data using "featurecount" from "Rsubread" packages, I used the DEseq2 to perform differential analysis.
Below is the scatter plot (WT vs CKO), I could obtain genomic region wit ...
written 2.1 years ago by
Wet&DryImmunology • 220
• updated
2.1 years ago by
Devon Ryan ♦ 91k
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Comment:
C: What does "gappedPeak" mean
... @Goutham Atla . Thanks, everything begins to make sense. ...
written 2.3 years ago by
Wet&DryImmunology • 220
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... Hi, I used "macs2" to call peaks from my data of ChIP-seq.
This is not my first time to use macs2, but still found myself not being able to grasp what "gappedPeak" stands for in the OUTPUT of macs2.
"NAME_peaks.narrowPeak" , "NAME_peaks.broadPeak" are quite intuitive,
"narrowPeak" means narrow ...
written 2.3 years ago by
Wet&DryImmunology • 220
• updated
2.3 years ago by
geek_y ♦ 9.8k
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... @EagleEye , Thanks for the explanation. I sort of fell into some logical trap.
Normally, people present data like this:
PeakA(a number) only --group a
PeakB(a number) only --group b
PeakA & PeakB (a number) --groub c
like:
![enter image description here][1]
I think it would be very e ...
written 2.4 years ago by
Wet&DryImmunology • 220
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... @EagleEye. Thanks, it works!
PS: I had another small issue.
after I called:
bedtools intersect -wao -a proteinA_cellX_peaks.broadPeaks -b H3K27ac_cellX_peaks.broadPeaks > common_regions.txt
I trie to confirm the result by:
wc -l proteinA_cellX_peaks.broadPeak
19559 pro ...
written 2.4 years ago by
Wet&DryImmunology • 220
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... Hi I guess this is a sort of naive question.
In some papers, there are some Venn diagrams showing the overlap of TFs/Histone modifications bound peaks.
I was wondering how they get the overlap. I checked the methods, but could not get the information, maybe this is too rudimentary that people eve ...
written 2.4 years ago by
Wet&DryImmunology • 220
• updated
2.4 years ago by
EagleEye ♦ 6.4k
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... @Jean-Karim Heriche. Yes, I am recompiling gcc from the source with fortran enabled. The "make" command takes very long time to finish... but I guess it would work out. Really appreciate your suggestion. ...
written 2.4 years ago by
Wet&DryImmunology • 220
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... Hi my primary goal is to use DiffBind to analyze my ChIPseq data.
Following the suggestion that I [might need to update my DiffBind][1]
I tried to install a new version of it.
By the checking the [dependency of DiffBind][2] I guess that the previous installation automatically install an old vers ...
written 2.4 years ago by
Wet&DryImmunology • 220
• updated
2.4 years ago by
Biostar ♦♦ 20
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... I see. Tks for patient explanation! ...
written 2.5 years ago by
Wet&DryImmunology • 220
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