I am using mitochondrial PacBio data and would like to know how to calculate the species-specific mutation rate of mitochondrial DNA for my species.? I humbly request guidance from all experts on this matter.
Please kindly correct me if I am mistaken in my approach.
Bundle of thanks in Advance!!
Best Regards,
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written
by
hashim.rana11 •
1 answer
We have not seen any information on your approach, so how can we evaluate it?
Here's what I would recommend: 1) Download and extract https://sourceforge.net/projects/bbmap/files/BBMap_39.09.tar.gz 2) Extract the mitochondrial sequence from the reference as mito.fa 3) Run mapPacBio.sh in=reads.fq out=mapped.sam ref=mito.fa bs=bs.sh ; sh bs.sh 4) Now you can look at it in IGV!
If you want something more precise, you will need to provide more details.
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