Editing
Dinh/Dinh 2012/NOTES/2012-2-27
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!
==Mapping bias to reference== * I extracted all heterozygous SNP calls from: /home/kunzhang/AfricanGenomes/Tishkoff15/dbSNPAnnotated-GS00319-DNA_C02_1100_37-ASM.tsv awk '{if($10 ~ /het/)print $0}' /home/kunzhang/AfricanGenomes/Tishkoff15/dbSNPAnnotated-GS00319-DNA_C02_1100_37-ASM.tsv > tmp & * I used this script to prepare chromosome 10 for bisulfite reads mapping: [[File:prepareAltGenome.txt]] ./prepareAltGenome.pl /media/1TB_store1/Rui_Scratch/iGenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa CAPB046_D02.hg19.hetSNP convert=yes context=cg ./prepareAltGenome.pl /media/1TB_store1/Rui_Scratch/iGenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa convert=yes context=cg /usr/local/soap/2bwt-builder var.genome.fa.bis.fwd /usr/local/soap/2bwt-builder var.genome.fa.bis.rev /usr/local/soap/2bwt-builder genome.fa.bis.fwd /usr/local/soap/2bwt-builder genome.fa.bis.rev /usr/local/samtools/samtools faidx var.genome.fa.bis.fwd /usr/local/samtools/samtools faidx var.genome.fa.bis.rev /usr/local/samtools/samtools faidx genome.fa.bis.fwd /usr/local/samtools/samtools faidx genome.fa.bis.rev * Then I mapped using bisReadMapper.pl (using the reads from PennAfrican_Batch1_Indx2_1.txt, note this is only half of the reads) nohup bisReadMapper_v1/bisReadMapper.pl CAPB46_D02.params > CAPB46_ref.log & nohup ../bisReadMapper_v1/bisReadMapper.pl CAPB46_D02.paramsVAR > CAPB46_var.log & * BisReadMapper.pl kept all the bam files, so I used samtools to convert to sam and counted the lines: 420926 ref.fwd.sam 416280 ref.rev.sam ================== 421103 var.fwd.sam (0.4% more reads mapped) 454589 var.rev.sam (9.2% more reads mapped) * Do reads which we missed when mapping to the reverse strand going to affect the final CpG measurements? * Correlation HuRef CpGs versus CAPB046 CpGs = 0.9997136 bedtools intersect -wao -a ref.methyl.cg-pos.BED.txt -b var.methyl.cg-pos.BED.txt | awk '{if($10 ~ /chr/) print $4"\t"$13;}' > refvsvar.values '''Calculate correlation using R''' * I also compared to Noi's B01_CAPB046.BED.txt file (this used all of the reads.) Just to validate that the new genome preparation script was not different from the pipeline that Noi is using. * My HuRef CpGs versus Noi's HuRef CpGs = 0.9911043 * Noi's HuRef CpGs versus CAPB046 CpGs = 0.9910447 ==Conclusion== * Reference genome mapping bias is only causing ~9% fewer reads getting mapped to the reverse complementary strand. ** Since we convert all Cs to Ts in the forward strand, the reduce complexity genome is less affected by C/T SNPs (since any C/T snps will be treated the same) ** However, for the reverse complementary strand, where there is a C/T SNP, there is a G (mismatch) to the actual A allele. * Correlation of CpG methylation values indicates little technical bias.
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