Methylation correlation between adjacent CpGs in certain genomic interval from BAM files

Hi All,

I was asked to calculate the correlation (Pearson) of the methylation between the adjacent CpGs with the reads from the BAM files (BS-seq). Any script or software?

Thanks. I have made the perl script.

Thanks

Best regards

bs-seq methylation correlation

• 2,218 views • link

updated 4.0 years ago by Ram

• written 10.7 years ago by Shicheng Guo

If you have got an answer, would you mind sharing it with the community so that folks can learn from your experience?

• 0 views • link

written 10.7 years ago by Sean Davis

0 answers

No answers yet.

More posts like this

Statistical test or method to test relationship between nearby genes and CpG sites
written 2.1 years ago by user911111111 •

Dear All , I have a list of CpG sites and the genes lying close to the CpG sites, the respective beta values and gene …
Calculate ChIP-seq correlation in promoter regions
written 7.4 years ago by dcheng1 •

I read a few papers that calculate Pearson correlation coefficient of ChIP-seq replicates **in promoter regions**. However, even for active marks like H3K4me3, not 100% …
McGill Epigenomics Mapping Centre BS-Seq Data Problem
written 8.0 years ago by Shicheng Guo

Hi All, I tried to download some BS-Seq data from [McGill Epigenomics Mapping Centre (\[Here Database Link\]\[1\])][1] I have a little assumption about the BS-Seq …
Definition and formula of methylation heterogeneity
written 10.3 years ago by Shicheng Guo

Dear All, Now everybody are talking about methylation heterogeneity? I just wonder what's methylation heterogeneity? Is there any specific definitions and Is there any formula …
Single-end vs Pair-end RRBS methyation sequencing
written 10.5 years ago by Shicheng Guo

Hi All, Here is the question. Considering the cost and the achievement of the methylation sequencing, Do you think single-end RRBS or BS-seq would be …
Haplotype Blocks inferring with Perl script (LD block inferring)
written 10.7 years ago by Shicheng Guo

Hi All, Is there any perl expert who has completed the perl script for LD (genetic) inferring? Can you share the script, Thanks. Best regards,
The best data format for to store BS-seq or RRBS dataset
written 10.7 years ago by Shicheng Guo

Hi All, Is there any suggestion which kind of intermediate data format would be nice to be use to save the BS-seq or RRBS dataset? …
Converting Phred64 fastq to Phred33 fastq
written 10.7 years ago by Shicheng Guo

Hi all, I've been asked to convert some Phred64 fastq files to Phred33 fastq How can I perform this? Any recommended perl script? Thank you …
Average Methylation Level for a Genomic Region from Bam File (PileOMeth )
written 10.8 years ago by Shicheng Guo

Hey colleagues, Is there any convenient method (one step process) to extract *average methylation level* for a specific genomic region from BAM files of BS-seq …
R: extract interest nucleotide from BAM files (BS-Seq)
written 10.9 years ago by Shicheng Guo

Hi colleagues, I want to extract the nucleotide (C or T) for each reads from BAM files (BS-Seq) in some interesting positions (CpG sites). Do …