Ylaine/2009-8-17: Difference between revisions

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>Ylaine
(New page: ==New 1K Genomes Reference== * Get 5 more matches and 5 fewer misses than when trio file used for comparison ** Should be more. Too many mismatches? Debugging code. ** Found bug: using re...)
 
>Ylaine
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==New 1K Genomes Reference==
==New 1K Genomes Reference==
* Get 5 more matches and 5 fewer misses than when trio file used for comparison
* BowtieMaq: Get 5 more matches and 5 fewer misses than when trio file used for comparison
** Should be more. Too many mismatches? Debugging code.  
** Should be more. Too many mismatches? Debugging code.  
** Found bug: using reference instead of 1K call for comparison  
** Found bug: using reference instead of 1K call for comparison  
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* Try with SOAP/SAM
../Scripts/compare1K.pl hiqual.no_dbSNP.het>hiqual.no_dbSNP.het.1K
** Place in separate folder
==New Data==
WorkSpace/Exome/Solexa/NA12878/NA12878_061009_061109_080509_081309_40bp_sequence.bowtie.pileup
===Part 1===
{{Quotation|What is the total size of exonic region that were covered by >=8x in this data set? For that you will need the pileup file which is available on genome-tech in my folder: WorkSpace/Exome/Solexa/NA12878/}}


==Thoughts about classification==
==Thoughts about classification==
* We need a universal classification scheme that doesn't rely on knowing the classes of the training set.
* We need a universal classification scheme that doesn't rely on knowing the classes of the training set.
* A more analogous problem is one of clustering
* A more analogous problem is one of clustering

Revision as of 20:38, 17 August 2009

New 1K Genomes Reference

  • BowtieMaq: Get 5 more matches and 5 fewer misses than when trio file used for comparison
    • Should be more. Too many mismatches? Debugging code.
    • Found bug: using reference instead of 1K call for comparison
../Scripts/hetOnly.pl no_dbSNP.new1K >no_dbSNP.new1K.het
  • Quality and coverage alone are the best combination of parameters
  • For n=50, p=0.3, f = 0.75:
' Mean Std
FP 25.26 7.32
MD 15.20 6.17
Overall 18.32 4.02
  • Try with SOAP/SAM
../Scripts/compare1K.pl hiqual.no_dbSNP.het>hiqual.no_dbSNP.het.1K
    • Place in separate folder

New Data

WorkSpace/Exome/Solexa/NA12878/NA12878_061009_061109_080509_081309_40bp_sequence.bowtie.pileup

Part 1

Template:Quotation

Thoughts about classification

  • We need a universal classification scheme that doesn't rely on knowing the classes of the training set.
  • A more analogous problem is one of clustering