Mitochondrial gene expression

Question

[bart]

Hi,

I have a gene count file of human samples and would like to know only the gene counts of all mitochondrial genes. Is there a list of ensemble gene ids of only the mitochondrial genes? Also, would it have been necessary to use a FASTA and/or GTF file with only information about mitochondrial genes or would it be better to use the FASTA and GTF file which includes all human genes? (I used the second option)

Thanks in advance!

[ATpoint]

Get the Ensembl GTF and subset to chromosome "M", then you have the mt genes.

[bart]

Thanks! I have found the genes. One question though: should I repeat transcript assembly with only this filtered GTF file of chrM genes using Stringtie/Cufflinks? Or can I immediately use the gene_ids of the mitochondrial genes from the filtered file?

Answer 1

[nn]

Have a look at this

https://www.broadinstitute.org/mitocarta/mitocarta30-inventory-mammalian-mitochondrial-proteins-and-pathways