User: mickey_95

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mickey_9510
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Posts by mickey_95

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Comment: C: DiffBind - normalization methods with biologically-relevant differences in signa
... I recently started using DiffBind for differential accessibility analysis of ATAC-seq. Could you elaborate more on why diffBind options are not robust and in which aspects csaw is better? I am still a newbie to this :) ...
written 9 days ago by mickey_9510
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Comment: C: DESeq2 design matrix
... I don't have access to the data at the moment, I will try to upload a picture later during the week. But in the meantime: How would I assess whether the experiment is underpowered using the MA plot? ...
written 13 days ago by mickey_9510
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Comment: C: DESeq2 design matrix
... These are primary cells from mice, control and drug-treated. The samples are all over the place in the PCA plot, there is no clear clustering of the two groups (ctrl and treated). I guess this variability could be the explanation? ...
written 13 days ago by mickey_9510
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Comment: C: DESeq2 design matrix
... Thank you for the quick reply! My technical replicates cluster closely together in a PCA plot, so I will collapse them. I ran de DESeq2 pipeline with the design you suggested and am very surprised to see that no differentially accessible regions pop up. This seems very strange to me and I do not und ...
written 13 days ago by mickey_9510
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DESeq2 design matrix
... Hi, I am trying to use DESeq2 for differential analysis of ATAC-seq data. I have performed peak calling, obtained a consensus peak data set and, using featureCounts, generated a count matrix with my samples as columns and the peak coordinates as rows. I have two conditions, 4 biological and 2 techn ...
deseq2 de analysis atac-seq written 17 days ago by mickey_9510 • updated 17 days ago by ATpoint25k
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Comment: C: Convert Granges list of peaks into consensus counts
... I just noticed something: When converting the imported peak regions to a GRanges object using myPeaks <- lapply(peaks, ChIPQC:::GetGRanges, simple = TRUE) the first line, i.e. peak, in each file does not get imported. Why is that? Or am I missing something? ...
written 6 weeks ago by mickey_9510
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Comment: C: Convert Granges list of peaks into consensus counts
... Thanks a lot for your help and effort! ...
written 6 weeks ago by mickey_9510
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Comment: C: Convert Granges list of peaks into consensus counts
... You can just append the code from the RU tutorial to the solution above, i.e. once you have the consensus list from above (stored in the variable reducedConsensus) you can do the following: consensusToCount <- reducedConsensus # for staying consistent with the naming of the variables in the RU t ...
written 6 weeks ago by mickey_9510
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ATAC-seq peak calling
... Hi Biostars community, I am new to ATAC-seq analysis, hence the following basic questions regarding the consensus in the field: Should I perform peak calling (I am using MACS2 in PE mode) using the entire BAM file or should I first split the BAM file in nucleosome free, mono-nucleosome, di-nucleos ...
peak calling macs2 atac-seq written 6 weeks ago by mickey_9510 • updated 6 weeks ago by ATpoint25k
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Comment: C: Convert Granges list of peaks into consensus counts
... Hi, I cam across the same problem when following the ATAC-seq tutorial from Rockefeller University (https://rockefelleruniversity.github.io/RU_ATAC_Workshop.html) and trying to run the same function, namely soGGi:::runConsensusRegions. I also always get NULL. So I tried using your solution/function ...
written 6 weeks ago by mickey_9510

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