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mapping to annotated mitochondria
Hi everyone,
I am new here and is still learning the most basic. I have been mapping RNA-seq reads to RefSeq as well as mm10 or mm9 genome. When mapping to the entire genome, I found some of the positions with the most reads belong to the mitochondrial genome (chrM), and this is only in samples from certain tissue but not others. So I am curious to find out how many reads are mapped to the chrM genes in this tissue. Where can I find references with annotated mouse chrM (RefSeq does not contain chrM genes)? Or should I build a reference based on information in Genbank NC_010339? Any other ideas would be appreciated.
Thanks in advance.
I am new here and is still learning the most basic. I have been mapping RNA-seq reads to RefSeq as well as mm10 or mm9 genome. When mapping to the entire genome, I found some of the positions with the most reads belong to the mitochondrial genome (chrM), and this is only in samples from certain tissue but not others. So I am curious to find out how many reads are mapped to the chrM genes in this tissue. Where can I find references with annotated mouse chrM (RefSeq does not contain chrM genes)? Or should I build a reference based on information in Genbank NC_010339? Any other ideas would be appreciated.
Thanks in advance.