Noi/NOTES/2012-1-24: Difference between revisions

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* 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>
3. Generated TPED file: GetTPED.txt[[Media:GetTPED.txt]]
3. Generated TPED file: GetTPED.txt[[Media:GetTPED.txt]]<br>
ls -l *pileup.snp.filtered > filtered.snp.list
ls -l *pileup.snp.filtered > filtered.snp.list

Revision as of 22:21, 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 helped 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

3. Generated TPED file: GetTPED.txtMedia:GetTPED.txt
ls -l *pileup.snp.filtered > filtered.snp.list