Noi/NOTES/2012-1-24

From ZhangLabWiki
Revision as of 23:11, 24 January 2012 by >Noi (Created page with '= UCLA (Schizophrenia) data analysis (continued) = == qMTL analysis == * Dr. Zhang suggested that we should start to do mQTL analysis with the SNP data we called by look at 2M or…')
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

UCLA (Schizophrenia) data analysis (continued)

qMTL 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.
  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;

  1. 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