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lecture_notes:05-03-2010 [2010/05/03 21:59]
svasili
lecture_notes:05-03-2010 [2010/05/08 18:11] (current)
galt Putting the Heng Li and R. Durbin paper in a proper reference format with link
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   - Biological tricks:   - Biological tricks:
     - c->​b->​a->​b'​->​d     - c->​b->​a->​b'​->​d
-    - an inversion of b->​a->​b'​ turns the scaffold into c->​b->​a'​->​b'​->​d...(I think this should be c->​b'​->​a'​->​b->​d)+    - an inversion of b->​a->​b'​ turns the scaffold into c->​b->​a'​->​b'​->​d... ​Note that flipping b->a->​b' ​reverses and complements the sequences, so that it becomes (b')->​a'​->​b' or b->a'​->​b'​.
  
 Burrows-Wheeler Transform (BWT) Burrows-Wheeler Transform (BWT)
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       - R-("​O"​) = c(O) + O("​O"​) + 1 = 6       - R-("​O"​) = c(O) + O("​O"​) + 1 = 6
       - R_("​GO"​) =        - R_("​GO"​) = 
-  - Kevin recommends reading the paper. ​[Fast and Accurate Short read alignment with Burrows-Wheeler ​Transform, ​Heng Li and Richard Durbin, bioinformatics ​2009]+  - Kevin recommends reading the paper. ​**Fast and accurate short read alignment with Burrows-Wheeler ​transform.**[(cite:​bwa>​Heng Li and Richard Durbin.\\ 
 +Bioinformatics. ​ 2009 Jul 15;​25(14):​1754-60. Epub 2009 May 18.\\ 
 +Wellcome Trust Sanger InstituteWellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.\\ 
 +doi:​[[http://​dx.doi.org/​10.1093/​bioinformatics/​btp324|10.1093/​bioinformatics/​btp324]
 +)] 
 + 
 + 
 + 
 +===== References ===== 
 +<​refnotes>​notes-separator:​ none</​refnotes>​ 
 +~~REFNOTES cite~~ 
 + 
lecture_notes/05-03-2010.1272949199.txt.gz · Last modified: 2010/05/03 21:59 by svasili