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]]
* Dinh: /home/dinh/UPenn_Analysis/UPenn48_April12/dbSNP130_hg18_filteredSNPs/
1. All .snp files were filtered with hg19 dbSNP using script written by Dr. Zhang in genome-miner: /home/kunzhang/bin/bisSnpFilterHg19.pl<br>
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>

Revision as of 07:48, 25 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]]
  • Dinh: /home/dinh/UPenn_Analysis/UPenn48_April12/dbSNP130_hg18_filteredSNPs/

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