# Banana Slug Genomics

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lecture_notes:05-03-2010

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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]galt Putting the Heng Li and R. Durbin paper in a proper reference format with link Both sides previous revision Previous revision 2010/05/08 18:11 galt Putting the Heng Li and R. Durbin paper in a proper reference format with link2010/05/04 07:26 karplus fixed mistaken comment about flipping b->a->b'2010/05/03 21:59 svasili 2010/05/03 15:14 hyjkim created Next revision Previous revision 2010/05/08 18:11 galt Putting the Heng Li and R. Durbin paper in a proper reference format with link2010/05/04 07:26 karplus fixed mistaken comment about flipping b->a->b'2010/05/03 21:59 svasili 2010/05/03 15:14 hyjkim created Line 12: Line 12: - 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) Line 95: Line 95: - 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 Institute, Wellcome 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 cite~~ +