Alignment based sizing of inserts

Smriti · 06-11-2012, 04:30 PM

Hi everyone,

I am new to the field of DNA sequencing. I need a quick help, can anyone explain me what do we mean by alignment based sizing of insert DNA and how different it is from physical size of the DNA. How do we calculate this alignment based size.

A quick help will be really appreciated, I have an impt. meeting tomo where I need this info.

Regards

ECO · 06-11-2012, 04:57 PM

Read up on paired end or mate-pair libraries.

The short answer is, by mapping reads derived from both ends of a molecule, one can "size" that molecule against the reference genome. If you know you made your library with 250bp physical molecules, and the ends of that molecule map 10kb apart in the reference genome, you can infer that your sample genome has a deletion.

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06-11-2012, 04:30 PM	#1
Smriti Member Location: California Join Date: Mar 2011 Posts: 40	Alignment based sizing of inserts Hi everyone, I am new to the field of DNA sequencing. I need a quick help, can anyone explain me what do we mean by alignment based sizing of insert DNA and how different it is from physical size of the DNA. How do we calculate this alignment based size. A quick help will be really appreciated, I have an impt. meeting tomo where I need this info. Regards

06-11-2012, 04:57 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Read up on paired end or mate-pair libraries. The short answer is, by mapping reads derived from both ends of a molecule, one can "size" that molecule against the reference genome. If you know you made your library with 250bp physical molecules, and the ends of that molecule map 10kb apart in the reference genome, you can infer that your sample genome has a deletion.