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

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m (Created page with '==Data Analysis== ===Read mapping=== Mapping script Amplicon # reads % uniquely mapped % non-unique % unmappable 1A…')
 
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     1F          7760883          65.75%          14.21%      20.04%
     1F          7760883          65.75%          14.21%      20.04%
     1G          5102454          52.91%            7.46%      39.62%
     1G          5102454          52.91%            7.46%      39.62%
===Looking for local enrichment of mapped reads.===
===Looking for local enrichment of mapped reads.===
*I used this [[File: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 [[File:getBlockCoverage.txt|script]] to group the per-site coverage into 10Mb windows, then visualize the average coverage using [http://www.ncrna.org/idiographica Idiographica].

Revision as of 00:59, 18 September 2010

Data Analysis

Read mapping

   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.

  • 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