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-edit.txt]]<br>
* '''mergeAndSplit.pl:''' [[Media:mergeAndSplit-edit.txt]]<br>
./mergeAndSplit.pl < all-GK0091-003.snp.filtered > GK0091-003.fwd.pileup.snp.filtered<br>
./mergeAndSplit.pl < all-GK0277-002.snp.filtered > GK0277-002.fwd.pileup.snp.filtered<br>
./mergeAndSplit.pl < all-GK0277-005.snp.filtered > GK0277-005.fwd.pileup.snp.filtered<br>
./mergeAndSplit.pl < all-GK0123-002.snp.filtered > GK0123-002.fwd.pileup.snp.filtered<br>
3. Generated TPED file: GetTPED.txt[[Media:GetTPED.txt]]<br>
3. Generated TPED file: GetTPED.txt[[Media:GetTPED.txt]]<br>
ls UCLA_filtered_SNP/*snp.filtered > list_snp<br>
ls UCLA_filtered_SNP/*snp.filtered > list_snp<br>
awk '{print "123"$0"123\t"$0;}' list_snp | sed 's/123UCLA_filtered_SNP\///g' | sed 's/.fwd.pileup.snp.filtered123//g' > filtered.snp_list<br>
awk '{print "123"$0"123\t"$0;}' list_snp | sed 's/123UCLA_filtered_SNP\///g' | sed 's/.fwd.pileup.snp.filtered123//g' > filtered.snp_list<br>

Revision as of 22:48, 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 helped me wrote script to merge the SNP data.

./mergeAndSplit.pl < all-GK0091-003.snp.filtered > GK0091-003.fwd.pileup.snp.filtered
./mergeAndSplit.pl < all-GK0277-002.snp.filtered > GK0277-002.fwd.pileup.snp.filtered
./mergeAndSplit.pl < all-GK0277-005.snp.filtered > GK0277-005.fwd.pileup.snp.filtered
./mergeAndSplit.pl < all-GK0123-002.snp.filtered > GK0123-002.fwd.pileup.snp.filtered
3. Generated TPED file: GetTPED.txtMedia:GetTPED.txt
ls UCLA_filtered_SNP/*snp.filtered > list_snp
awk '{print "123"$0"123\t"$0;}' list_snp | sed 's/123UCLA_filtered_SNP\///g' | sed 's/.fwd.pileup.snp.filtered123//g' > filtered.snp_list