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.
- To merge and sort the chromosome position: cat GK* | sort -k1,1 > all.GK.snp.filtered
- mergeAndSplit.pl: Media:mergeAndSplit-edit.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 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