I am not a professional bioinformatics and just a PhD student happen appeared in the genetic lab. I am very interested in your sQTLseekeR program in finding SNP-related transcript shifts. Based on previous results in our lab (RNA-seq and Illumina genotype data), we calculated estimated counts and imputated genotypes for some risk-related SNPs. To include the coordination information, I also extracted genotypes for some LD (linkage disequilibrium) SNPs (R2>0.9, same genotype distribution with risk-related SNP). Can I still use sqtl function to filter out the results? And in fact, when I tried to run sqtl, it nearly gives 5 candidate association and keep error for "spine infinite or missing error".
Hello jmonlong,
I am not a professional bioinformatics and just a PhD student happen appeared in the genetic lab. I am very interested in your sQTLseekeR program in finding SNP-related transcript shifts. Based on previous results in our lab (RNA-seq and Illumina genotype data), we calculated estimated counts and imputated genotypes for some risk-related SNPs. To include the coordination information, I also extracted genotypes for some LD (linkage disequilibrium) SNPs (R2>0.9, same genotype distribution with risk-related SNP). Can I still use sqtl function to filter out the results? And in fact, when I tried to run sqtl, it nearly gives 5 candidate association and keep error for "spine infinite or missing error".
Thank you!
Yijun