Has anybody had a few samples of RNA seq where > 70% of the mapped reads match mitochondria? What's going on?
Background : I got 68 bam files for a disease (can't go into details: HIPPA secrecy concerning pediatric patients in USA .. and all that). Processing used the novoalign RNA vignette using hg19 and November 2012 refseq.
Three of the *darn* samples really stuck out because they had lots of RNA expression reads mapped to chrM (mitochondria). A lot of other reads mapped to that chr1 area of mitochondrial similarity near the tip of chr1p. The rest of the mapped reads seemed to make sense; i.e. a very small bump at a gene that shows much expression in other samples.
Has anybody seen this? Is it real? What's going on? Are there really cells where RNA expression is 80% mitochondria ?
Background : I got 68 bam files for a disease (can't go into details: HIPPA secrecy concerning pediatric patients in USA .. and all that). Processing used the novoalign RNA vignette using hg19 and November 2012 refseq.
Three of the *darn* samples really stuck out because they had lots of RNA expression reads mapped to chrM (mitochondria). A lot of other reads mapped to that chr1 area of mitochondrial similarity near the tip of chr1p. The rest of the mapped reads seemed to make sense; i.e. a very small bump at a gene that shows much expression in other samples.
Has anybody seen this? Is it real? What's going on? Are there really cells where RNA expression is 80% mitochondria ?
Comment