6 votes
Accepted

How to understand methylation level?

You are right that a single molecule in a single position is either methylated or not methylated. However: First, assuming your organism of interest is diploid (or of higher ploidy) one of the ...
6 votes

Melt p-values for CpG sites mapping to the same gene

Methylation levels have high local correlation, so Fisher's method would be problematic. Having said that, you have no reason to use Fisher's method after a paired t-test. A paired t-test will give ...
  • 19.3k
6 votes
Accepted

What are some good practices to follow during EPIC DNA methylation data analysis?

EPIC data can be processed in the same manner as the previous iteration of methylation array data from Illumina (450k). This means that starting with .idat files, normalization should be performed (...
  • 397
5 votes
Accepted

How many types of DNA methylation are there?

If I'm understanding you correctly, by "types of DNA methylation" you mean "nucleotide contexts where DNA methylation occurs". This is going to be a function of the methyltransferase proteins involved ...
  • 1,222
4 votes

Identify differentially covered genes only between two samples

Not really an answer but an extended comment... and most likely something you don't like to hear I guess by technical replicates, it means taking the same biological sample and making 2 methylation ...
  • 1,648
4 votes
Accepted

Inflated p-values in quantitative trait analysis

Permutation as suggested by @StupidWolf's comment is essential to understand what's going on. If permutation makes this pattern go away, then you have a problem with your model specification, there's ...
4 votes
Accepted

Highlight CpG sites with Texshade

The best solution I could find was to use the \shaderegion function on all the sequences so it ended up looking something like this: ...
  • 255
4 votes
Accepted

How to interpret methylation calls from Bismark on opposite strands?

The strand the bismark reports is related to the strand from which the read originated, not necessarily how it's aligned. So, alignments on the + strand shouldn't have calls overlapping those on the - ...
  • 19.3k
3 votes
Accepted

Best way to detect long insertions in bisulfite sequencing data?

You'd be best off by starting with -rfg and -rdg as is and reverting bismark's change of ...
  • 19.3k
2 votes
Accepted

alternatives to MEDIPS to analyse MeDIP datasets

I guess QSEA should be an obvious answer: QSEA (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA ...
  • 2,099
2 votes

Recommendations for missing value imputation - DNA methylation data

I think this is still an active field of research. I have heard of Phenix, which might be appropriate.
  • 2,116
2 votes

Continuing analysis based on a log-likelihood ratio? (Comparing methylation between two PoolSeq phenotypes)

I assume you don't want to spend 1-2 years developing your own method based on nanopore data, so the path forward is to convert the output into a format used by standard DMR calling programs. There's ...
  • 19.3k
2 votes

WGBS vs ONT, which one should I trust?

Methylation can be cell-specific, which makes it difficult to evaluate accuracy on a bulk-cell level (even within the same tissue). How can you tell that the differences you're seeing are due to ...
  • 12k
2 votes

Methylation data: beta values are normally distributed

$\beta$ values are the ratio of methylated to unmethylated probe intensities. This means that $\beta \in [0, 1]$, so it can't be normally distributed, by definition. Its distribution may have sections ...
  • 1,222
1 vote

ambiguous calls in nanopolish

Assuming that it is the postprocessing script calculate_methylation_frequency.py that you are using, user Wouter de Coster's comment is correct that the methylation ...
1 vote

WGBS vs ONT, which one should I trust?

I would assess directionality and accuracy of prediction by 1) WGBS predicting ONT and then 2) ONT predicting WGBS. Firstly, I would use deep learning (or machine learning) and train WGBS against ONT, ...
  • 7,980
1 vote

Defining methylation level of CpG island

In my experience, the most common approach to find DMR is to use the DSS R package to call and merge DML into regions. DMC/DML (Differential Methylation Cytosine/...
1 vote

Question: Bismark methylation for non-uniquely mapping BS-seq reads

I'm not certain about your piRNA approach, maybe others will be able to help with that question. As for multi-mapped reads, from Bismark's documentation you can find the ...
  • 1,222
1 vote
Accepted

Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19)

You can get specific sequences efficiently using the following packages: ...
1 vote

Identify differentially covered genes only between two samples

You may run edgeR for methylation analysis without replicates (https://f1000research.com/articles/6-2055). But I also recommend you to have a look at the R DSS package (http://bioconductor.org/...
1 vote

Error in createMAE function: non-unique values when setting 'row.names' in TCGA LIHC Data

The error message is pretty clear: R requires unique row names on data frames and some of the "values" that you are trying to set as row names are non-unique. You will need to provide a vector i) of ...
  • 3,507
1 vote
Accepted

DNA bioinformatic search and methylation analysis by qMSP

It's likely that they accomplished this by using the UCSC Table Browser to: Find the loci of the two isoforms you mention Finding CpG islands (Group = Regulation, Track = CpG Islands) near those ...
  • 1,222
1 vote

Extract LINE-1 methylation status from WGBS data

Via BEDOPS: $ bedmap —-echo —-echo-map-id-uniq <(bam2bed < reads.bam) <(rmsk2bed < repeats.rmsk) > answer.bed
1 vote

Extract LINE-1 methylation status from WGBS data

After a more extensive search, I found a useful answer that I'll share in case anyone else wonders how to do this. I'm using MethylKit package for differential methylation expression and it is quite ...
  • 395
1 vote

Melt p-values for CpG sites mapping to the same gene

What is typically done in methylation analysis is to assess the islands of methylations. Check this workflow, in the section linked it uses some predefined islands for instance. I am no expert on ...
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