Jeff:LabNotes/Microbiome/2010-12-8: Difference between revisions
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==Data Analysis of HL079 Data (Chromosomes)== | ==Data Analysis of HL079 Data (Chromosomes)== | ||
''MDA completed on 8-19-2010[:http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-8-19] | |||
===Read mapping=== | ===Read mapping=== | ||
Used scripts provided by Dr Zhang | Used scripts provided by Dr Zhang | ||
[[Media:variantCallerBowtieSamSimple.txt|Mapping script]] | [[Media:variantCallerBowtieSamSimple.txt|Mapping script]] | ||
Amplicon # reads % uniquely mapped % non-unique % unmappable | Amplicon # reads % uniquely mapped % non-unique % unmappable | ||
1B | 1B | ||
1C | 1C | ||
1D | 1D | ||
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==Major conclusions== | ==Major conclusions== | ||
*Samples 1C and 1D have 2-3 chromosomes | *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 1B seems to have some coverage on many chromosomes. There must be a lot of fragments. 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 | *Sample 2G has only fragments. This sample was diluted 10x from the other samples |
Latest revision as of 01:51, 10 December 2010
Data Analysis of HL079 Data (Chromosomes)[edit]
MDA completed on 8-19-2010[:http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2010-8-19]
Read mapping[edit]
Used scripts provided by Dr Zhang Mapping script Amplicon # reads % uniquely mapped % non-unique % unmappable 1B 1C 1D 2G
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:Sample1Bcov.png Sample 1B File:Sample1Ccov.png Sample 1C File:Sample1Dcov.png Sample 1D File:Sample2Gcov.png Sample 2G
SNP distribution[edit]
- I extracted variants from the pileup files using pileup2variants, then plot the distribution of known SNPs using this script and Idiographica.
File:Sample1Bsnps.png Sample 1B File:Sample1Csnps.png Sample 1C File:Sample1Dsnps.png Sample 1D File:Sample2Gsnps.png Sample 2G
Major conclusions[edit]
- Samples 1C and 1D have 2-3 chromosomes
- Sample 1B seems to have some coverage on many chromosomes. There must be a lot of fragments. 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