Questions tagged [methylation]

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Volcano Plot: How to show unique gene names in the plot?

I'm wondering how can I show unique gene names in the volcano plot. My data looks like, ...
Deb's user avatar
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DNA methylation mediator analysis for environmental exposure and health outcome

We measured blood DNA methylation using epic array in 100 no-diabetic and 100 type 1 diatbetic patients matched for age, sex and smoking and also measured arsenic exposure using ICP-MS. Could you ...
bioinfonext's user avatar
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Enrichment analysis of DMPs | new Ilumina EPIC V2 900K

Im analyzing methylation data from the new illumina's EPIC V2 array (900K). I would like to perform enrichment analysis on DMPs. In the past, I have always used missMethyl but since there are a lot of ...
Julieta's user avatar
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1 answer
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Read methylation data from tar files on GEO (GSE73303)

I'm trying to analyise methylation data using GEO, in order to conduct a multi-omics analysis. The SubSeries I am referring to is GSE73303. Unfortunately, the code used to inspect it produces empty ...
Riesz98's user avatar
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datasets or biobanks with both (WGS or genotype intensity) and methylation data

My aim is to associate CNVs to DNAm, but I don't know where to find datasets which contain both (sequencing + methylation). Do you know any?
Caterina's user avatar
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1 answer
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Can bwameth accept unaligned Bam?

Does bwameth accept bam (unaligned) type as input or I will have to convert unaligned bam to fastq (samtools fastq bam) to use ...
aerijman's user avatar
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2 votes
0 answers
48 views

PCA of methylation-values normalized by coverage

I have started analyzing methylation (EM-seq) data for the first time ~0.8M positions. In this data set I have 27 samples of 20 patients. I want to perform a PCA of the dataset to check for possible ...
llrs's user avatar
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How do I intrepret the generated motifs of a dataset of 5-methylcytosine (5mC) sequences?

I'm a computer science person currently working on a project which uses deep learning to identify 5mC sites of Nipponbare Rice. Within the project, there is an option to view what the model 'discovers'...
EnigmaticCocoon's user avatar
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Is there a generally accepted method used to impute missing DNA methylation data (probe beta-values)?

I'm looking at DNA methylation (DNAm) data such as TCGA (e.g., BRCA, KIRP, KIRC, etc.). Currently trying to build use my model to predict DNAm age on test sets, but many of the data sets are missing ...
sumthymes's user avatar
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2 answers
215 views

Methylation data: beta values are normally distributed

I am trying to incorporate Methylation data (Illumina 450K) into my pipeline. I was provided with two versions of the same data: one (dataset $a$) normalized with ComBat and the other (dataset $b$) ...
wrong_path's user avatar
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1 answer
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How to determine a correct promoter sequence? (Bisulfite sequencing)

I'd like to ask you for help with an university assignment. First let me post the entire question: Design primers for bisulfite sequencing of the promoter of the ACE2 gene in microbat Myotis ...
Matěj Nemec's user avatar
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ambiguous calls in nanopolish

I am converting scores into frequencies (from nanopolish results) using Nanopore scripts. The script filters out lots of rows on the premise that reads where ...
aerijman's user avatar
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How to use EPIC DNAm files (.idat) to infer copy number alteration

I have access to EPIC DNA methylation profiles from approximately 40 samples. I want to use these .idat files in order to predict copy number alterations within specific promoter regions of interest. ...
gb0413's user avatar
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2 votes
2 answers
100 views

WGBS vs ONT, which one should I trust?

First of all let me apologize if this is not the place for this question. While it can be quite broad, I will try to make it as specific as I can. Context I am testing the correlation between Whole ...
Paul Endymion's user avatar
2 votes
1 answer
71 views

Defining methylation level of CpG island

Differentially methylated site is technically measured by each probe. However, CpG island within gene promoter is comprised of numerous probes. Do we have a consensus of how to determine the ...
unicorn's user avatar
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1 answer
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How to understand methylation level?

For Bisulfite Sequencing data, we can calculate methylation level for a specific locus, $$ \mbox{methylation level} = \frac{\mbox{# methelyated reads}}{\mbox{# total reads}} $$ Here I think, for this ...
Jie's user avatar
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1 answer
230 views

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

I am looking for the DNA methylation, specifically inside small RNAs; piRNA. I am mapping BS-seq reads on the genome with bismark. From the user guide of bismark, it maps reads uniquely on the genome, ...
kashiff007's user avatar
3 votes
1 answer
237 views

Inflated p-values in quantitative trait analysis

I am performing a quantitative trait association between the expression of one gene and ~400,000 methylation values. First, both variables are rank inverse normal transformed, adjusted for confounders ...
sergiovm's user avatar
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1 answer
325 views

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

I have a problem in R. I have the following dataSet (the first three rows shown) (the 5th number is the methylation level in its region): ...
Giannis Lazaridis's user avatar
1 vote
2 answers
42 views

Identify differentially covered genes only between two samples

I have a question about finding differentially covered regions (coverage represents methylation level which goes from 0 to several thousands). I'm using enrichment based method which can be summarized ...
pogibas's user avatar
  • 203
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1 answer
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Error in createMAE function: non-unique values when setting 'row.names' in TCGA LIHC Data

I am working with the createMAE() function of the ELMER Bioconductor package. While executing the createMAE() function using ...
J. Smith's user avatar
1 vote
0 answers
51 views

How can I get the estimate of lmFit function form limma package

This is the first time that I used lmfit function from the limma package I'm a little bit confused on how to interpret the result. is there a way to get the ...
Mr.M's user avatar
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1 vote
1 answer
202 views

How many types of DNA methylation are there?

My current understanding is: bases A or C can become methylated due to interaction with a methyltransferase these methylations ...
TimD1's user avatar
  • 302
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1 answer
38 views

DNA bioinformatic search and methylation analysis by qMSP

Im quoting the methods which was used We performed a bioinformatics analysis to identify potential CpG islands in the genomic sequences of RANKL and OPG genes. The USCS Human Genome Browser ...
kcm's user avatar
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3 votes
0 answers
266 views

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: ...
Hayley Sowards's user avatar
1 vote
0 answers
148 views

Bismark report before and after Cytosine Methylation Extraction

Looking at the sample report from Bismark webpage, there are two sections: Cytosine Methylation and Cytosine Methylation after Extraction. However even after reading User Guide, I still cannot ...
user44697's user avatar
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1 vote
1 answer
136 views

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

I'm trying to get some pointers on where to start on the analysis of my dataset. First, some basic info: Background: We performed Nanopore sequencing of two poolseq samples called UU and DD referring ...
dfarr's user avatar
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8 votes
1 answer
62 views

dog coordinates (canFam3) to human coordinates (hg19)

I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...
Alex Stuckel's user avatar
3 votes
1 answer
63 views

Highlight CpG sites with Texshade

I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? ...
quantik's user avatar
  • 255
4 votes
1 answer
358 views

Recommendations for missing value imputation - DNA methylation data

I'm looking for some options for imputation for a high-dimensional dataset of DNA methylation (bisulfite sequencing) data. Dimensions on the order of 50-100 samples x ~500,000 CpG loci/features. I'...
Reilstein's user avatar
  • 367
3 votes
3 answers
109 views

Extract LINE-1 methylation status from WGBS data

I've been trying to figure out the correct way of extracting methylation status of particular elements from WGBS data, and found several possible approaches, but would like to discuss which one could ...
Kraken's user avatar
  • 405
8 votes
2 answers
80 views

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

I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
user1309's user avatar
4 votes
1 answer
82 views

Best way to detect long insertions in bisulfite sequencing data?

I am interested in identifying indels in whole genome bisulfite sequencing data (76bp paired end). Currently, I do this by setting the -rfg and ...
Ben D.'s user avatar
  • 397
3 votes
1 answer
443 views

How to interpret methylation calls from Bismark on opposite strands?

I'm looking at Reduced representation bisulfite sequencing (RRBS) data from ENCODE, and to align the FASTQ files I've used Bismark with Bowtie 1. When I load the resulting BAM file into ...
James Hawley's user avatar
  • 1,384
3 votes
0 answers
179 views

Minfi returning incorrect beta values

UPDATE: I found the solution. I was using normalized values and GEO was using raw beta values. I'm trying to link GEOquery and minfi. Specifically I want to obtain beta values from the idat files ...
Ezra Bekele's user avatar
4 votes
1 answer
71 views

alternatives to MEDIPS to analyse MeDIP datasets

MEDIPS is an established tool with functions for the quality control and analysis of data derived from immunoprecipitation (IP)-seq samples, like Methylation IP sequencing datasets. I would like to ...
719016's user avatar
  • 2,324
6 votes
1 answer
554 views

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

I recently got some EPIC DNA methylation data and I was wondering what are some good practices to follow? I am interested in knowing about normalization and differential analysis. Thank you.
deepseas's user avatar
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