Kun:LabNotes/Haplotyping/2010-9-17: Difference between revisions

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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:GM20431_chr_1A.blockCoverage.png|600px]]
   [[Image:GM20431_chr_1A.blockCoverage.png|400px]]
   [[Image:GM20431_chr_1F.blockCoverage.png|600px]]
   [[Image:GM20431_chr_1F.blockCoverage.png|400px]] [[Image:GM20431_chr_1G.blockCoverage.png|400px]]
  [[Image:GM20431_chr_1G.blockCoverage.png|600px]]
===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].
   [[Media:GM20431_chr_1A_SNP_dist.png|600px]]
   [[Image:GM20431_chr_1A_SNP_dist.png|400px]]


==Major conclusions==
==Major conclusions==
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*The chromosome concentration was over-estimated by roughly three folds.  
*The chromosome concentration was over-estimated by roughly three folds.  
*Compared with purified gDNA, the amplification curves on chromosomes tend to shoot up earlier. Therefore, we can't use the amplification curves on purified gDNA to estimate the number of chromosomes in each reaction.
*Compared with purified gDNA, the amplification curves on chromosomes tend to shoot up earlier. Therefore, we can't use the amplification curves on purified gDNA to estimate the number of chromosomes in each reaction.
*Three chromosomes were present in the Amplicon 1A (small chromosomes, 10 chr/reaction). It is very likely that the other three amplicons (1B,1C,1D) from the same batch are good too.
*Three chromosomes (5,12,19) were present in the Amplicon 1A (amplified from small chromosomes, 10 chr/reaction). It is very likely that the other three amplicons (1B,1C,1D) from the same batch are good too.
*Amplicons 1F and 1G were amplified from small DNA fragments, and not usable.

Latest revision as of 01:44, 18 September 2010

Data Analysis[edit]

Read mapping[edit]

   Mapping script
   Amplicon    # reads    % uniquely mapped  % non-unique  % unmappable 
   1A          7613296          66.42%           14.39%       19.20%
   1F          7760883          65.75%           14.21%       20.04%
   1G          5102454          52.91%            7.46%       39.62%

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:GM20431 chr 1A.blockCoverage.png
  File:GM20431 chr 1F.blockCoverage.png File:GM20431 chr 1G.blockCoverage.png

SNP distribution[edit]

  File:GM20431 chr 1A SNP dist.png

Major conclusions[edit]

  • Amplification from diluted chromosomes is an viable option.
  • The chromosome concentration was over-estimated by roughly three folds.
  • Compared with purified gDNA, the amplification curves on chromosomes tend to shoot up earlier. Therefore, we can't use the amplification curves on purified gDNA to estimate the number of chromosomes in each reaction.
  • Three chromosomes (5,12,19) were present in the Amplicon 1A (amplified from small chromosomes, 10 chr/reaction). It is very likely that the other three amplicons (1B,1C,1D) from the same batch are good too.
  • Amplicons 1F and 1G were amplified from small DNA fragments, and not usable.