paired-end vs. mate-pair

lre1234 · 11-18-2011, 04:07 AM

Hi all,
we are planning on doing some whole genome sequencing and I have a question. I have been under the impression that paired-end sequencing is the best method to use, but now some of the people here are telling me that we should use mate-pair.

While I know the differences between the two methods, I am not sure which is the best one to use. Does anyone have any thoughts on which one is better, or know of a pub that has compare the two methods?

Thanks for your help and thoughts.

HESmith · 11-18-2011, 06:38 AM

Mate-pair is a specific type of library; paired-end is a type of sequencing. They are not two different methods; in fact, mate-pair libraries require paired-end sequencing.

The decision to use mate-pair vs. standard libraries depends upon your application.

swbarnes2 · 11-18-2011, 08:26 AM

Mate pair allows you to have your pairs be much farther apart, which can be more informative than the standard paired-end protocol.

The downside is that it's a more complicated protocol, and it can be contaminted with ordinary paired-end reads, which I image can make analysis more difficult.

krobison · 11-18-2011, 05:28 PM

The other class of challenge from mate pair data are false mates -- cases in which the ligation step brings two unrelated molecules together. The panda genome paper is an example where this was a very serious issue.

cw11 · 11-20-2011, 06:56 AM

This site describes some of the potential restrictions of the mate-pair library. I also found in this thread:

Quote:

Originally Posted by flobpf

I think paired end refers to sequencing from the ENDS of a DNA fragment. If you're doing 75-bp paired end read using an insert size of 300bp, then the machine will sequence 1-75 and 300-225 (for simplicity, omitting the adapters)

Mate pair requires a completely different protocol and is typically over longer distances such as 2-5kb. If you want to sequence a 5kb mate pair library, then 5kb fragments of DNA are isolated on the gel, the ends are biotinylated, the fragment is circularized and sheared. So now when you select using streptavidin, you'll get the fragment that has the ENDS of the original 5kb fragment. This fragment is then sequenced.

Mate pair is more relevant in genome assembly, especially for covering repetitive sequences. Paired end can be used for anything - RNA, DNA.

You can get more information on the Illumina site:
http://www.illumina.com/technology/p...ing_assay.ilmn

http://www.illumina.com/technology/m...ing_assay.ilmn

I'm not sure how 454 or other methods define these terms

meganathan.pr · 12-09-2011, 07:22 AM

Hi all,
I am trying to prepare mate pair library. I dont wanna use Illumina kit as it is costlier. Do any one have the protocol using other chemical supplies? can I get it?

Thanks

masker · 12-10-2011, 07:00 AM

I remember that because of the single read length, the 454 defined "paired-end" as "mate-pair" from Illumina.

SEQond · 04-05-2013, 05:17 AM

I find Illumina's explanation for paired-end quite lacking. Wikipedia has a better explanation

chevrm · 04-05-2013, 05:25 AM

Mate-pairs are wonderful if you're dealing with particularly tricky assemblies, CNVs, or looking for other structural variations (translocs, etc) but may not be worth it if you don't have any of these criteria.

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11-18-2011, 04:07 AM	#1
lre1234 Member Location: US Join Date: Aug 2011 Posts: 29	paired-end vs. mate-pair Hi all, we are planning on doing some whole genome sequencing and I have a question. I have been under the impression that paired-end sequencing is the best method to use, but now some of the people here are telling me that we should use mate-pair. While I know the differences between the two methods, I am not sure which is the best one to use. Does anyone have any thoughts on which one is better, or know of a pub that has compare the two methods? Thanks for your help and thoughts.

12-09-2011, 07:22 AM	#6
meganathan.pr Junior Member Location: Starkville Join Date: Oct 2011 Posts: 3	Hi all, I am trying to prepare mate pair library. I dont wanna use Illumina kit as it is costlier. Do any one have the protocol using other chemical supplies? can I get it? Thanks __________________ Meganathan

11-18-2011, 06:38 AM	#2
HESmith Senior Member Location: Washington DC Join Date: Oct 2009 Posts: 280	Mate-pair is a specific type of library; paired-end is a type of sequencing. They are not two different methods; in fact, mate-pair libraries require paired-end sequencing. The decision to use mate-pair vs. standard libraries depends upon your application.

11-18-2011, 08:26 AM	#3
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 766	Mate pair allows you to have your pairs be much farther apart, which can be more informative than the standard paired-end protocol. The downside is that it's a more complicated protocol, and it can be contaminted with ordinary paired-end reads, which I image can make analysis more difficult.

11-18-2011, 05:28 PM	#4
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 682	The other class of challenge from mate pair data are false mates -- cases in which the ligation step brings two unrelated molecules together. The panda genome paper is an example where this was a very serious issue.

12-10-2011, 07:00 AM	#7
masker Junior Member Location: Taiwan Join Date: Mar 2010 Posts: 1	I remember that because of the single read length, the 454 defined "paired-end" as "mate-pair" from Illumina.

04-05-2013, 05:17 AM	#8
SEQond Member Location: Italy Join Date: Jul 2010 Posts: 27	I find Illumina's explanation for paired-end quite lacking. Wikipedia has a better explanation

04-05-2013, 05:25 AM	#9
chevrm Junior Member Location: Boston, MA Join Date: Apr 2012 Posts: 4	Mate-pairs are wonderful if you're dealing with particularly tricky assemblies, CNVs, or looking for other structural variations (translocs, etc) but may not be worth it if you don't have any of these criteria.