Ylaine/2009-8-17: Difference between revisions
Jump to navigation
Jump to search
>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 |
||
Line 1: | Line 1: | ||
==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 | ||
Line 20: | Line 20: | ||
| | | | ||
|} | |} | ||
* 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
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