Novomethyl comments

Gen2007 · 01-13-2011, 01:40 PM

Has anyone implemented novomethyl for methylation calling in their research? What are your thoughts/comments? Do you like it?

Up until now I have used my own scripts to call methylation status from bisulfite reads, but am considering novomethyl.

simonandrews · 01-14-2011, 12:47 AM

That's not a name I'd seen before and there doesn't seem to be much information about it even on the Novocraft web site.

We use (and wrote) Bismark for doing both bisulphite alignment and methylation calling in a single step. We did this because, as you found, although there are a number of decent aligners around it's not always easy to convert the alignments into a set of methylation calls - especially if it's important to you that methylated and unmethylated reads are mapped with comparable efficiencies.

Nix · 01-14-2011, 01:14 PM

Wasn't aware Colin and crew were building such tools! Will check them out.

I've built a variety of apps for processing novoalign bisulfite reads, single end or paired into the USeq package. (See the Bis seq apps section : http://useq.sourceforge.net/applications.html )

BisStat takes a single methylome and generates xxCxx context statistics and graph tracks for IGB. It also identifies mCs using a binomial pval -> B&H FDR

BisSeq takes two methylomes and identifies differentially methylated regions using a chi-square/ fischer-exact -> B&H FDR.

ScoreMethylatedRegions uses a permuation test to look for differences in methylation between a user defined list of regions and a matched background.

Attached is a screen shot of some reprocessed data from Laurent et. al. showing differentially methylated regions (ES vs Fibro) at the tbx2 locus.

zee · 03-21-2011, 02:45 AM

A new version of novomethyl has been released. Colin has also written quite an extensive guide for methylation calling that I would highly recommend you'll check out.
The latest version of novomethyl can be downloaded from www.novocraft.com. We are going to do some validation against Bismark in the near future.

Gen2007 · 03-23-2011, 12:29 PM

Thanks a lot zee. Please let us know when you've finished/published the validation against Bismark. Thanks!

slp · 04-20-2012, 09:41 AM

Hi Zee,
Have you already validated novomethyla against BismArk. I am using novomethyl fo my methylC-seq data and cn't find any publication that has use novomethyl.

zee · 04-20-2012, 07:13 PM

Hi Slp and Gen2007
The short answer is no we have not done an extensive comparison of the two systems. Bismark is alignment+methylation caller so the best way to compare would be against novoalign(bisulfite)+novomethyl.
Bismark should be using Bowtie2. It will good for somebody to do a fair, unbiased comparison.

01-13-2011, 01:40 PM	#1
Gen2007 Member Location: St. Louis Join Date: Jun 2010 Posts: 10	Novomethyl comments Has anyone implemented novomethyl for methylation calling in their research? What are your thoughts/comments? Do you like it? Up until now I have used my own scripts to call methylation status from bisulfite reads, but am considering novomethyl.

01-14-2011, 12:47 AM	#2
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	That's not a name I'd seen before and there doesn't seem to be much information about it even on the Novocraft web site. We use (and wrote) Bismark for doing both bisulphite alignment and methylation calling in a single step. We did this because, as you found, although there are a number of decent aligners around it's not always easy to convert the alignments into a set of methylation calls - especially if it's important to you that methylated and unmethylated reads are mapped with comparable efficiencies.

01-14-2011, 01:14 PM	#3
Nix Member Location: SLC, Utah Join Date: Jun 2008 Posts: 60	Wasn't aware Colin and crew were building such tools! Will check them out. I've built a variety of apps for processing novoalign bisulfite reads, single end or paired into the USeq package. (See the Bis seq apps section : http://useq.sourceforge.net/applications.html ) BisStat takes a single methylome and generates xxCxx context statistics and graph tracks for IGB. It also identifies mCs using a binomial pval -> B&H FDR BisSeq takes two methylomes and identifies differentially methylated regions using a chi-square/ fischer-exact -> B&H FDR. ScoreMethylatedRegions uses a permuation test to look for differences in methylation between a user defined list of regions and a matched background. Attached is a screen shot of some reprocessed data from Laurent et. al. showing differentially methylated regions (ES vs Fibro) at the tbx2 locus.

03-21-2011, 02:45 AM	#4
zee NGS specialist Location: Malaysia Join Date: Apr 2008 Posts: 249	A new version of novomethyl has been released. Colin has also written quite an extensive guide for methylation calling that I would highly recommend you'll check out. The latest version of novomethyl can be downloaded from www.novocraft.com. We are going to do some validation against Bismark in the near future.

03-23-2011, 12:29 PM	#5
Gen2007 Member Location: St. Louis Join Date: Jun 2010 Posts: 10	Thanks a lot zee. Please let us know when you've finished/published the validation against Bismark. Thanks!

04-20-2012, 09:41 AM	#6
slp Junior Member Location: NY, USA Join Date: Dec 2010 Posts: 9	Hi Zee, Have you already validated novomethyla against BismArk. I am using novomethyl fo my methylC-seq data and cn't find any publication that has use novomethyl.

04-20-2012, 07:13 PM	#7
zee NGS specialist Location: Malaysia Join Date: Apr 2008 Posts: 249	Hi Slp and Gen2007 The short answer is no we have not done an extensive comparison of the two systems. Bismark is alignment+methylation caller so the best way to compare would be against novoalign(bisulfite)+novomethyl. Bismark should be using Bowtie2. It will good for somebody to do a fair, unbiased comparison.