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Questions tagged [methylation]

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1answer
48 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 ...
0
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1answer
28 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 ...
3
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0answers
127 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: ...
1
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0answers
47 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 ...
1
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1answer
36 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 ...
3
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0answers
18 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 ...
3
votes
1answer
51 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? ...
4
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1answer
274 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'...
3
votes
3answers
59 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 ...
8
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2answers
50 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. ...
4
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1answer
60 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 ...
3
votes
1answer
256 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 ...
3
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0answers
94 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 ...
3
votes
1answer
34 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 ...
5
votes
1answer
320 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.