Kun:LabNotes/Haplotyping/2010-9-17: Difference between revisions
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[[Image:GM20431_chr_1F.blockCoverage.png|600px]] | [[Image:GM20431_chr_1F.blockCoverage.png|600px]] | ||
[[Image:GM20431_chr_1G.blockCoverage.png|600px]] | [[Image:GM20431_chr_1G.blockCoverage.png|600px]] | ||
===SNP distribution=== | |||
*I extracted variants from the pileup files using [[]], then plot the distribution of known SNPs using [[Media:plotSNPs.txt|this script]] and [http://www.ncrna.org/idiographica Idiographica]. | |||
==Major conclusions== | ==Major conclusions== |
Revision as of 01:33, 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
SNP distribution
- I extracted variants from the pileup files using [[]], then plot the distribution of known SNPs using this script and Idiographica.
Major conclusions
- 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 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.