mitochondrial genes

[ZoeG]

I am interested in but not familiar with mitochondrial genes.
Here are questions regarding how to determine the expression of mitochondrial genes in RNASeq data.

1) In UCSC's reference genome for mouse (mm10, mm9..), how can I tell whether a gene is a mitochondrial gene? In the 'chromosome' column, I found chr1~19, chrX, but not 'chrM'. Does that mean that mitochondrial genes are not involved or I need find mitochondrial genes by another way?

2) It is said that mitochondrial genes are relatively short. If I map my data to mitochondrial reference gtf directly, I may get a lot of mis-matches which are actually other genes rather than mitochondrial genes. What's the recommended way to map mitochondrial genes?

3) This question is TopHat related. I am using TopHat to map RNASeq data. If I want to map the data to mitochondrial genes, what's the easiest way ? Could I just generate a GTF for mitochondrial genes, then use TopHat to map data to this GTF? Do I need also modify bowtie reference?

Thanks for your time to go through these questions,

[mastal]

mitochondrial genes

Hi,

In answer to part 1) of your question, I'm not sure why you don't have chrM,
it is listed on the UCSC downloads page for mm10, by chromosome.

http://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/

[ZoeG]

Hi,

In answer to part 1) of your question, I'm not sure why you don't have chrM,
it is listed on the UCSC downloads page for mm10, by chromosome.


http://hgdownload.cse.ucsc.edu/golde...0/chromosomes/

Due to the compatibility of the tool that I am using, I have to use mm9.
I got UCSC mm9 from http://tophat.cbcb.umd.edu/igenomes.shtml.
The first colunm is chromosome. It seems ChrM is not in the list.
So, maybe simply, mitochondrial genes are not included in the list for this version?