How to find the mutation rate per nucleotide in aligned RNA sequences
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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!

RNA-Seq mutation rate alignment • 1.2k views
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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).

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I am aligning RNA sequences. I am going to calculate the mutation rate in each nucleotide position. Thank you.

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Where did this sequence come from? What are you aligning it to?

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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.

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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!

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