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