Editing
Kun:LabNotes/Haplotyping/2010-9-17
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
==Data Analysis== ===Read mapping=== [[Media:variantCallerBowtieSamSimple.txt|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 [[Media:getBlockCoverage.txt|script]] to group the per-site coverage into 10Mb windows, then visualize the average coverage using [http://www.ncrna.org/idiographica Idiographica]. [[Image:GM20431_chr_1A.blockCoverage.png|400px]] [[Image:GM20431_chr_1F.blockCoverage.png|400px]] [[Image:GM20431_chr_1G.blockCoverage.png|400px]] ===SNP distribution=== *I extracted variants from the pileup files using [[Media:pileup2variants.txt|pileup2variants]], then plot the distribution of known SNPs using [[Media:plotSNPs.txt|this script]] and [http://www.ncrna.org/idiographica Idiographica]. [[Image:GM20431_chr_1A_SNP_dist.png|400px]] ==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 (5,12,19) were present in the Amplicon 1A (amplified from small chromosomes, 10 chr/reaction). It is very likely that the other three amplicons (1B,1C,1D) from the same batch are good too. *Amplicons 1F and 1G were amplified from small DNA fragments, and not usable.
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information