User: Wet&DryImmunology

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Japan
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Posts by Wet&DryImmunology

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Verification of Global Reduction of Epigenetic Factors ?
... @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 18 months ago by Wet&DryImmunology200
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Verification of Global Reduction of Epigenetic Factors ?
... 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 ...
R next-gen chip-seq written 18 months ago by Wet&DryImmunology200 • updated 18 months ago by Devon Ryan86k
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Comment: C: What does "gappedPeak" mean
... @Goutham Atla . Thanks, everything begins to make sense. ...
written 21 months ago by Wet&DryImmunology200
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What does "gappedPeak" mean
... 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 ...
enocde macs2 chip-seq written 21 months ago by Wet&DryImmunology200 • updated 21 months ago by geek_y8.8k
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Comment: C: Identification of commonly bound regions by TFs/histone modification/other featu
... @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 22 months ago by Wet&DryImmunology200
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Comment: C: Identification of commonly bound regions by TFs/histone modification/other featu
... @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 22 months ago by Wet&DryImmunology200
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Identification of commonly bound regions by TFs/histone modification/other features
... 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 ...
bedtools sequence chip-seq written 22 months ago by Wet&DryImmunology200 • updated 22 months ago by EagleEye6.0k
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Comment: C: Issue when trying to install 'RcppArmadillo': /usr/bin/ld: cannot find -lgfortra
... @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 22 months ago by Wet&DryImmunology200
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Issue when trying to install 'RcppArmadillo': /usr/bin/ld: cannot find -lgfortran
... 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 ...
software error chip-seq written 22 months ago by Wet&DryImmunology200 • updated 21 months ago by Biostar ♦♦ 20
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Comment: C: Problem when trying to extract column value using "awk" from txt table
... I see. Tks for patient explanation! ...
written 22 months ago by Wet&DryImmunology200

Latest awards to Wet&DryImmunology

Popular Question 20 months ago, created a question with more than 1,000 views. For From Cuffdiff Output to CummeRbund analysis/visualisation
Popular Question 22 months ago, created a question with more than 1,000 views. For From Cuffdiff Output to CummeRbund analysis/visualisation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For From Cuffdiff Output to CummeRbund analysis/visualisation
Student 2.4 years ago, asked a question with at least 3 up-votes. For Peak callers for ChIP seq comparison
Appreciated 2.5 years ago, created a post with more than 5 votes. For Peak callers for ChIP seq comparison
Good Question 2.5 years ago, asked a question that was upvoted at least 5 times. For Peak callers for ChIP seq comparison
Student 2.6 years ago, asked a question with at least 3 up-votes. For Peak callers for ChIP seq comparison

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