Currently i am working on a project related to LHON disease (rare mitochondrial disorder which leads to progressive visual loss).
I have 9 RNA-seq fastq files out of which 3 are for carriers, 3 for affected and 3 for control. Data downloaded is taken from here link
To do read mapping for this dataset what should I take as reference genome (human reference genome or mitochondrial reference genome)
After doing read mapping I have to generate read counts to apply DeSeq2 on it.
If I'm using mitochondrial reference genome to align the fastq files then in further steps I'll need annotation file (gtf) to get read counts. But I'm unable to find annotation file of mitochondrial genome. How can I get this annotation file for mitochondrial genome?
And my other query is: can i use human reference genome(hg38) for read mapping because annotation file for this genome is available and then generate read counts.
Please tell me which approach will be better.