Noi/NOTES/2012-1-24: Difference between revisions
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* Dr. Zhang suggested that we should start to do mQTL analysis with the SNP data we called by look at 2M or 5M window. | * Dr. Zhang suggested that we should start to do mQTL analysis with the SNP data we called by look at 2M or 5M window. | ||
* Dinh's link for mQTL analysis on UPenn Data: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-29]] | * Dinh's link for mQTL analysis on UPenn Data: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-29]] | ||
1. All .snp files were filtered with hg19 dbSNP using script written by Dr. Zhang in genome-miner: /home/kunzhang/bin/bisSnpFilterHg19.pl<br> | |||
'''snpFilter.sh'''<br> | '''snpFilter.sh'''<br> | ||
<br> | <br> | ||
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/home/kunzhang/bin/bisSnpFilterHg19.pl $f > $f.filtered<br> | /home/kunzhang/bin/bisSnpFilterHg19.pl $f > $f.filtered<br> | ||
done;<br> | done;<br> | ||
2. There are 4 files that were mapped separately since the .fastq files are very large. Dinh help me wrote script to merge the SNP data.<br> | |||
* To merge and sort the chromosome position: cat GK* | sort -k1,1 > all.GK.snp.filtered | * To merge and sort the chromosome position: cat GK* | sort -k1,1 > all.GK.snp.filtered | ||
* '''mergeAndSplit.pl:''' [[Media:mergeAndsplit.txt]]<br> | * '''mergeAndSplit.pl:''' [[Media:mergeAndsplit.txt]]<br> |
Revision as of 23:14, 24 January 2012
UCLA (Schizophrenia) data analysis (continued)
mQTL analysis
- Dr. Zhang suggested that we should start to do mQTL analysis with the SNP data we called by look at 2M or 5M window.
- Dinh's link for mQTL analysis on UPenn Data: [[1]]
1. All .snp files were filtered with hg19 dbSNP using script written by Dr. Zhang in genome-miner: /home/kunzhang/bin/bisSnpFilterHg19.pl
snpFilter.sh
for f in *.snp
do
/home/kunzhang/bin/bisSnpFilterHg19.pl $f > $f.filtered
done;
2. There are 4 files that were mapped separately since the .fastq files are very large. Dinh help me wrote script to merge the SNP data.
- To merge and sort the chromosome position: cat GK* | sort -k1,1 > all.GK.snp.filtered
- mergeAndSplit.pl: Media:mergeAndsplit.txt