I have 10X scRNA-seq data for a hESC and after the alignment using cellrenger, I used seurat V3 to cluster cells. Since this is a normal cell line, I expected not to see any clusters of cells. However, the mt% in seurat is VERY strange
and has 2 clusters which finally results in getting 2 separate clusters in the final scRNA-seq analysis (I only keeo mt%< 6). Is such mt% normal? removing 2-6 mt% will reduce the reads from 500,000 to 15,000 and does not seem right! removing 0-2% mt and keeping 2-6 %mt also does not look right to me.
Any suggestions why there is such mt%? Is it only experiment problem? if not, how should I treat it so that i will not lose a lot of reads.