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 ...
- 1,464
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 ...
- 19.8k
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 ...
- 1,394
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 ...
- 4,252
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 ...
- 1,698
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 - ...
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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 ...
- 19.8k
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 ...
- 2,209
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.
- 2,286
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 ...
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2
votes
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. It has a smoothing step which ...
2
votes
Accepted
Can bwameth accept unaligned Bam?
No, it's a bwa mem wrapper for bisulfite data essentially and bwa mem accepts fastq only.
- 1,511
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 ...
- 1,394
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 ...
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1
vote
Volcano Plot: How to show unique gene names in the plot?
Based on your comments, you wish to obtain a semi-colon separated list of unique values in the gene column. You can create a new column containing these using:
...
- 2,498
1
vote
Enrichment analysis of DMPs | new Ilumina EPIC V2 900K
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vignette: https://www.bioconductor.org/packages/release/bioc/...
- 11
1
vote
Read methylation data from tar files on GEO (GSE73303)
As I've already told you here GEO Methylation dataset "GSE73303" shows 0 features GEO/GEOquery does not provide ready-to-use processed NGS data. It can be that the authors provide processed ...
- 1,511
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/...
- 392
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 ...
- 4,252
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, ...
M__♦
- 13k
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 ...
- 1,394
1
vote
Accepted
Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19)
You can get specific sequences efficiently using the following packages:
...
- 126
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 ...
- 4,202
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 ...
- 1,394
1
vote
dog coordinates (canFam3) to human coordinates (hg19)
Based on this old answer, this is not recommended for liftOver. For between-species liftovers, it is claimed that you are likely to want a different tool such as pslMap. For a lot of rather detailed ...
- 4,252
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
- 3,184
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 ...
- 405
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