Question: Difference Between "Mate Pair" And "Pair-End"
gravatar for weiqiangduan
6.2 years ago by
weiqiangduan130 wrote:

Just as the title , I can't tell the difference between those two conception. :) waiting for your help.

paired-end ngs library • 28k views
ADD COMMENTlink modified 4.8 years ago by Biostar ♦♦ 20 • written 6.2 years ago by weiqiangduan130

Did you try google? The first hit for "mate-pair vs paired-end" explains it:

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Devon Ryan92k
gravatar for Malachi Griffith
6.2 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

Refer to Figures 6B and 6C on page 5 of this PDF: Illumina Genomic Sequencing Datasheet

ADD COMMENTlink written 6.2 years ago by Malachi Griffith17k

Updated link:

ADD REPLYlink written 3.9 years ago by Leandro Lima930


ADD REPLYlink written 3.6 years ago by pinakin760

thanks, it helps a lot

ADD REPLYlink written 19 months ago by lffu_003240
gravatar for swbarnes2
6.2 years ago by
United States
swbarnes26.7k wrote:

"Paired end" is pretty straight forward, you make fragments, you sequence both ends, and you have some knowledge of the distribution of fragment sizes in your library, so that helps you properly map.

One might want to make a library of 2 kb long fragments, so that you could get paired end data where each end is expected to be about that far from the other end, but there are practical reasons why you can't. Mate pair preps are designed to get around this. It's a more involved process that involves doing a lot of stuff so that in the end, you have 500 bp fragments, but the sequence at each end originated from regions of the reference that are much farther apart.

ADD COMMENTlink written 6.2 years ago by swbarnes26.7k
gravatar for Damian Kao
6.2 years ago by
Damian Kao15k
Damian Kao15k wrote:

In terms of the resulting sequenced data, they are pretty much the same thing. Although you might be able to argue that the quality of pairing might differ.

They differ in library preparation. In pair-end sequencing, the machine is sequencing the ends of a fragment. So if you have a 500bp fragment, you machine will sequence 1-75 and 425-500 of the fragment. In mate-pair libraries, you are creating a library of fragment ends and then performing normal sequencing on these end fragments,

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Damian Kao15k
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