Jeff:LabNotes/Microbiome/2010-12-8
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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
- I extracted variants from the pileup files using pileup2variants, then plot the distribution of known SNPs using this script and Idiographica.
[Image:sample1Bsnps.png|400px]] Sample 1B File:Sample1Bsnps.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