Noi/NOTES/2012-1-24
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-e.txt
./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 and tfam files: 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
- Still have some problem when running plink. The error message said about the number of column didn't match with the expected number of column. Need to figure out why it expected the wrong number.