Jeff:LabNotes/Microbiome/2010-12-8: Difference between revisions

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==Data Analysis of HL079 Data (Chromosomes)==
==Data Analysis of HL079 Data (Chromosomes)==


''MDA completed on 8-19-2010[[Media:http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-8-19]]
''MDA completed on 8-19-2010[:http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-8-19]


===Read mapping===
===Read mapping===
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     [[Media:variantCallerBowtieSamSimple.txt|Mapping script]]
     [[Media:variantCallerBowtieSamSimple.txt|Mapping script]]
     Amplicon    # reads    % uniquely mapped  % non-unique  % unmappable  
     Amplicon    # reads    % uniquely mapped  % non-unique  % unmappable  
     1B        
     1B            
     1C           
     1C           
     1D           
     1D           
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==Major conclusions==
==Major conclusions==
*Samples 1C and 1D have 2-3 chromosomes
*Samples 1C and 1D have 2-3 chromosomes
*Sample 1B seems to have many chromosomes.  Looking back to the real time curve, it seems that this one spiked up quicker.  Thus, there was most likely a dilution error
*Sample 1B seems to have some coverage on many chromosomes.  There must be a lot of fragments.  Looking back to the real time curve, it seems that this one spiked up quicker.  Thus, there was most likely a dilution error
*Sample 2G has only fragments.  This sample was diluted 10x from the other samples
*Sample 2G has only fragments.  This sample was diluted 10x from the other samples

Latest revision as of 01:51, 10 December 2010

Data Analysis of HL079 Data (Chromosomes)[edit]

MDA completed on 8-19-2010[:http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-8-19]

Read mapping[edit]

   Used scripts provided by Dr Zhang
   Mapping script
   Amplicon    # reads    % uniquely mapped  % non-unique  % unmappable 
   1B             
   1C          
   1D          
   2G          


Looking for local enrichment of mapped reads.[edit]

  • I used this script to group the per-site coverage into 10Mb windows, then visualize the average coverage using Idiographica.
  File:Sample1Bcov.png  Sample 1B      File:Sample1Ccov.png  Sample 1C
  File:Sample1Dcov.png Sample 1D File:Sample2Gcov.png  Sample 2G

SNP distribution[edit]

  File:Sample1Bsnps.png  Sample 1B      File:Sample1Csnps.png  Sample 1C
  File:Sample1Dsnps.png Sample 1D File:Sample2Gsnps.png  Sample 2G

Major conclusions[edit]

  • Samples 1C and 1D have 2-3 chromosomes
  • Sample 1B seems to have some coverage on many chromosomes. There must be a lot of fragments. Looking back to the real time curve, it seems that this one spiked up quicker. Thus, there was most likely a dilution error
  • Sample 2G has only fragments. This sample was diluted 10x from the other samples