Question: Is my understanding of mapping direction right?
0
gravatar for wangyi2412
5.2 years ago by
wangyi2412220
China
wangyi2412220 wrote:

Assume that the sample DNA sequence has no reverse mutation, the mapping result expected should be like this: 

                               5'                                                                      

template to seq      X1X2X3X4..........................................................................Xn-3Xn-2Xn-1Xn   

  (for example)        |------------------------------------------------------------------------------------------------->|

      reads                5'---------->3'                                                                                 3'<----------5'    

                               X1X2X3X4                                                                          X'n-3X'n-2X'n-1X'n

so assuming /1 corresponds to 5->3 of the template, /2 correspond to the 5->3 of the complementary strand of the template: 

the output reads of the strand coming from the ref strand should be:

/1(template 5->3)   X1X2X3X4...

/2(other end of the template, reversed complementary, 5->3)  X'nX'n-1X'n-2X'n-3

similarly, the output reads of strand coming from the alt strand should be:

/1(template 5->3)    X'nX'n-1X'n-2X'n-3

/2(other end of the template, reversed complementary, 5->3)       X1X2X3X4...

Right? 

No mater which strand the template comes from and the 1/2 labeling definition,  the output reads always start with 5', and the 5' are always at the outsider of the template, which means:

reads are always like this:

 

template: |------------------------------------------------------------------------------------------------->|

reads:      5'---------->3'                                                                                 3'<----------5' 

instead of this:

template: |------------------------------------------------------------------------------------------------->|

reads:      3'<----------5'                                                                                    5'--------->3' 

  

right? 

Thank you!  

    

exome-seq alignment • 1.0k views
ADD COMMENTlink written 5.2 years ago by wangyi2412220
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