Entering edit mode
4.5 years ago
npeng
▴
10
Hi,
I am now calculating the mutation rate per nucleotide per of the aligned RNA sequences (same virus specie but different strains). I am wondering what is the common tools/programs/package/algorithms to do this calculation so that the result will be more scientific since in my raw data there is no such a reference sequence as is mentioned in literature. Any useful information about the relevant paper or tools will be highly appreciated.
Thank you!
You are aligning DNA sequence (unless you are directly sequencing RNA on nanopore), correct? What are you using to do the alignments? How do you calculate width/depth of coverage you have? How are you accounting for sequencing error (which should be small with Illumina reads but won't be zero).
I am aligning RNA sequences. I am going to calculate the mutation rate in each nucleotide position. Thank you.
Where did this sequence come from? What are you aligning it to?
Sequences come from NCBI. I used MAFFT to align them. I am seeking for help to do the next step which is to calculate the mutation rate per nucleotide.
A: Mutation Rates calculation
C: Mutation Rates For A Specific Gene?
Thank you for the links. But I am trying to compute the mutation rate in each nucleotide position but not overall mutation rate. Do we have mature algorithms to do that or do I need to write my own codes to calculate that? Thank you!