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Hi all, I am re-doing methylation analysis using the updated ilm10b4 annotation with EPIC data (rather than ilm10b2) and after cleaning the data and normalisation, when i get to mapping to genome usin…
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## Description
As a bioinformatician, I would like to see what the DNA methylation looks like across all cells in a data set, in a small-ish region, in order to see the data underlying DMRs, enrich…
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Hi, I am new to nanodisco and methylation profile analysis in general. I have come across the same issue multiple times while trying to perform methylation binning on a nanopore sequenced dataset comp…
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Please provide as much information as you can:
* **GO term ID label:**
GO:0035516 broad specificity oxidative DNA demethylase activity IEA with PTHR16557:SF2
GO:0035552 oxidative single-strand…
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The current implementation of all and trans ranges does not need modification.
The logic for cis and distal regions are the same. The analyses utilize the parameters window_base, downstream, and up…
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Hello, I want to report that when I'm running my analysis, I'm getting the following error:
Error in dimnames(x) warnings()
Warning messages:
1: The dot-dot notation (`..count..`) was deprecated…
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Hi Felix,
I have a couple of questions regarding Bismark. I'm sorry if they are stupid questions; I am fairly new to WGBS data and Bismark analysis (or to bioinformatics in general).
We are rese…
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## Progress Report of Bloodies
#### What has changed based on the final proposal
We are using the same datasets as proposed but has eliminated a few samples from the analysis. For example, we remov…
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Hi,
I'm testing this pipeline on some EM-seq samples we have recently generated and getting following error with TSS_cpg_bins.py
File "/Software/EM-seq/TSS_cpg_bins.py", line 254, in
normal_…
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Hi,
met a problem with ChIPseeker recently.
The first one is the region priority problem with "genomicAnnotationPriority"
My question is:
when I use genomicAnnotationPriority = c("3UTR", "…