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[:http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-8-19]
 
===Read mapping===
===Read mapping===
     Used scripts provided by Dr Zhang
     Used scripts provided by Dr Zhang
     [[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         7613296          66.42%          14.39%      19.20%
     1B            
     1C          7760883          65.75%          14.21%      20.04%
     1C           
     1D          5102454          52.91%            7.46%      39.62%
     1D           
     2G           
     2G           


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===Looking for local enrichment of mapped reads.===
===Looking for local enrichment of mapped reads.===
*I used this [[Media:getBlockCoverage.txt|script]] to group the per-site coverage into 10Mb windows, then visualize the average coverage using [http://www.ncrna.org/idiographica Idiographica].
*I used this [[Media:getBlockCoverage.txt|script]] to group the per-site coverage into 10Mb windows, then visualize the average coverage using [http://www.ncrna.org/idiographica Idiographica].
   [[Image:sample1Bcov.png|400px]]  Sample 1B      [[Image:sample1Bcov.png|400px]]  Sample 1C
   [[Image:sample1Bcov.png|400px]]  Sample 1B      [[Image:sample1Ccov.png|400px]]  Sample 1C
   [[Image:sample1Dcov.png|400px]] Sample 1D [[Image:sample2Gcov.png|400px]]  Sample 2G
   [[Image:sample1Dcov.png|400px]] Sample 1D [[Image:sample2Gcov.png|400px]]  Sample 2G
===SNP distribution===
===SNP distribution===
*I extracted variants from the pileup files using [[Media:pileup2variants.txt|pileup2variants]], then plot the distribution of known SNPs using [[Media:plotSNPs.txt|this script]] and [http://www.ncrna.org/idiographica Idiographica].
*I extracted variants from the pileup files using [[Media:pileup2variants.txt|pileup2variants]], then plot the distribution of known SNPs using [[Media:plotSNPs.txt|this script]] and [http://www.ncrna.org/idiographica Idiographica].
   [[Image:sample1Bsnps.png|400px]]  Sample 1B      [[Image:sample1Bsnps.png|400px]]  Sample 1C
   [[Image:sample1Bsnps.png|400px]]  Sample 1B      [[Image:sample1Csnps.png|400px]]  Sample 1C
   [[Image:sample1Dsnps.png|400px]] Sample 1D [[Image:sample2Gsnps.png|400px]]  Sample 2G
   [[Image:sample1Dsnps.png|400px]] Sample 1D [[Image:sample2Gsnps.png|400px]]  Sample 2G


==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