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Getting Started

Getting Started. Download and install Haploview http://www.broad.mit.edu/mpg/haploview/index.php. Lab 1. Downloading dense genotype/resequencing data from HapMap and SeattleSNPs Choosing tagSNPs by using Haploview. Yu-Chun Jean Yen yyen@hsph.harvard.edu Bldg.2 Rm. 200.

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Getting Started

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  1. Getting Started • Download and install Haploview http://www.broad.mit.edu/mpg/haploview/index.php

  2. Lab 1 • Downloading dense genotype/resequencing data from HapMap and SeattleSNPs • Choosing tagSNPs by using Haploview Yu-Chun Jean Yenyyen@hsph.harvard.eduBldg.2 Rm. 200

  3. HapMap: http://www.hapmap.org/ Seattle SNPs: http://pga.mbt.washington.edu/ “Prettybase Purifier” tool: http://innateimmunity.net/IIPGA2/index_html(register required) Haploview:http://www.broad.mit.edu/mpg/haploview/index.php

  4. Click Here

  5. Search IGF1

  6. Zoom In

  7. Using HapMap.Org : A Tutorial http://www.hapmap.org/downloads/presentations/hapmap.org.ppt ASHG 2007 HapMap Tutorial http://www.hapmap.org/downloads/presentations/ASHG07_HapMapTutorial.ppt

  8. Click Here Select “Download SNP genotype data”

  9. Choose Click Here

  10. Click Here

  11. Click Here

  12. Right click to save

  13. “Prettybase” format SNP (relative pos) Subject Alleles Contains insertion-deletion polymorphisms (INDELS) 079773 E008 G G 079773 E009 G G 079773 E010 C C 079773 E011 G G 079773 E012 G G 079773 E013 C C 079773 E014 C G 079773 E015 G G 079773 E016 G G 079773 E017 C G 079773 E018 C G 079773 E019 C G 079773 E020 G G 079773 E021 G G 079773 E022 C C 079773 E023 N N 080761 D001 aa aa 080761 D002 aa - 080761 D003 aa aa 080761 D004 aa aa 080761 D005 aa aa 080761 D006 aa aa 080761 D007 aa aa 080761 D008 aa aa 080761 D009 aa aa 080761 D010 aa - 080761 D011 aa aa 080761 D012 aa aa 080761 D013 aa aa This can be a problem for many software tools, which expect SNPs – also indels present genotyping difficulties Can clean file using “prettybase purifier” tool at http://innateimmunity.net/IIPGA2/index_html (register required)

  14. Click Here

  15. Click Here

  16. Can restrict subjects to a given ethnicity Can restrict SNPs to those with MAF above a user-defined threshold Can eliminate INDELS

  17. “Prettybase” format SNP (relative pos) Subject Alleles Contains insertion-deletion polymorphisms This can be a problem for many software tools, which expect SNPs – also indels present genotyping difficulties Can clean file using “purifier” tool at http://innateimmunity.net/IIPGA2/index_html. 079773 E008 G G 079773 E009 G G 079773 E010 C C 079773 E011 G G 079773 E012 G G 079773 E013 C C 079773 E014 C G 079773 E015 G G 079773 E016 G G 079773 E017 C G 079773 E018 C G 079773 E019 C G 079773 E020 G G 079773 E021 G G 079773 E022 C C 079773 E023 N N 080761 D001 aa aa 080761 D002 aa - 080761 D003 aa aa 080761 D004 aa aa 080761 D005 aa aa 080761 D006 aa aa 080761 D007 aa aa 080761 D008 aa aa 080761 D009 aa aa 080761 D010 aa - 080761 D011 aa aa 080761 D012 aa aa 080761 D013 aa aa Many software tools don’t like this format Haploview, for example, wants “pedigree” file (short and fat instead of long and skinny) and “info” file (with SNP positions). Can convert using makehv (R function) or %haploview (SAS Macro), available at http://www.hsph.harvard.edu/faculty/kraft/soft.htm. [caveat emptor: this code is unsupported!]

  18. ped.idsubject.iddad.idmom.idgenderaffection.statussnp1.allele1snp1.allele2 etc.

  19. Click Here

  20. Click Here

  21. Click Here

  22. Force Include: have to genotype this SNP [e.g. nsSNP] Force Exclude: cannot genotype this SNP [e.g. known not to genotype well in your lab] Can combine “force include” and “force exclude” to evaluate how well a given set of SNPs performs Can decide what r2 performance you are willing to live with, whether you want to pursue “aggressive” tags Click Here

  23. SNPs you should genotype, tests you should perform How many SNPs does the highlighted marker “tag”

  24. Law of diminishing returns: you have to do a lot of genotyping to capture last few stragglers

  25. ped file info file

  26. Getting ready for next Lab session • Request IT Help Desk for a Unix Account.IT Helpdesk (LL-15) from 8:00 – 5:00pm, at 617-432-HELP, or helpdesk@hsph.harvard.edu. • Unix computing guide for beginners: http://www.isites.harvard.edu/icb/icb.do?keyword=k2067&pageid=icb.page23341

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