Hi,

I am working with 20 Illumina Paired End – 150 bp samples, basically, these are harvested tumor cells. Is there a way to identify mitochondrial contamination or other contamination data?

It seems that it would indeed be at the level of alignment QC, it is for instance possible to check for mitochondrial DNA contamination. Look at the raw reads mapping to transcriptome or not. So we can look the transcriptome mapping rate first then the rest to see if those reads not mapping to RNA map to DNA.

Does FastQC or MultiQC or any other approach provide any clue about the same?

Best Regards,

Toufiq