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

From ZhangLabWiki
Jump to navigation Jump to search
>Jgole
No edit summary
>Jgole
No edit summary
Line 16: Line 16:
===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



Revision as of 01:19, 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          7613296          66.42%           14.39%       19.20%
   1C          7760883          65.75%           14.21%       20.04%
   1D          5102454          52.91%            7.46%       39.62%
   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:Sample1Bcov.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