Go Back   SEQanswers > Applications Forums > Epigenetics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Bismark Methyl-seq Analysis Juulluu21 Bioinformatics 1 06-29-2017 01:43 AM
Miseq questions from a newbie Neiltje Illumina/Solexa 7 02-20-2014 06:05 AM
Questions about Bismark and bisulfite-seq sero Bioinformatics 4 07-11-2013 12:09 PM
Methyl-Seq Questions mariebreen Epigenetics 0 02-12-2013 01:21 PM

Thread Tools
Old 07-25-2018, 03:43 AM   #1
Junior Member
Location: France Rennes

Join Date: Jul 2018
Posts: 1
Default Newbie questions about Methyl-Seq (Bismark)


I'm quite new to epigenetics and DNA methylation data analysis, so many excuses in advance if my questions seem too naive or have already been answered elsewhere.

I was recently charged with analysis of Targeted bisulfite sequencing data of human patients.

Patients were sequenced on 3 different runs.
They used Illumina's TruSeq MethylCapture EPIC Library prep kit (107 Mb, 3,340,894 CpG sites) and the sequencing was performed on a NextSeq 500. The data is paired-end (fastq R1 + fastq R2).

After the initial QC (fastQC) and adapter trimming (Trim Galore!), I aligned my fastqs on a reference genome (UCSC hg19). I used Bismark tool (0.19.0) for Alignment, Deduplication and Methylation calling.
All patients were analysed with the same workflow.

What concerns me is a big difference of bismark reports between the runs (PDFs attached), especially the deduplication rate (75% for run1!) and CHG/CHH methylation (nothing for run2).

I don't really know what to make of this, and how much it will affect the downstream analysis. I'm very new to Methyl-Seq but the ultimate goal is to perform a case-control study to identify Differentially Methylated CpG Sites (I was thinking of using methylkit).

Am I doing something wrong or is it the problem with the initial data?

Any insight will be appreciated.
Attached Files
File Type: pdf Run_1.pdf (799.8 KB, 9 views)
File Type: pdf Run2.pdf (766.3 KB, 5 views)

Last edited by Freg; 07-26-2018 at 01:56 AM. Reason: Attachments
Freg is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:19 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO