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)==
===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           



Revision as of 01:23, 10 December 2010

Data Analysis of HL079 Data (Chromosomes)

Read mapping

   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.

  • 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

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

Major conclusions

  • 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 2G has only fragments. This sample was diluted 10x from the other samples