I'd like to know why you're taking the following filtering criteria. "For each tSNP, an individual was filtered out if the minor allele count was less than 5, or the total read count was less than 20, or the minor allele count was less than 5% of the total read count." In my mind, if the total read count (RNA-seq read count) is large than 20 and minor allele read count is less than 5% of the total read count, this scenario can be caused by allelic expression imbalance as the minor allele has been suppressed. Thank you in advance.
Dear @Jiaxin-Fan
I'd like to know why you're taking the following filtering criteria. "For each tSNP, an individual was filtered out if the minor allele count was less than 5, or the total read count was less than 20, or the minor allele count was less than 5% of the total read count." In my mind, if the total read count (RNA-seq read count) is large than 20 and minor allele read count is less than 5% of the total read count, this scenario can be caused by allelic expression imbalance as the minor allele has been suppressed. Thank you in advance.
Best wishes, Zheng zhuqing