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M__ ♦
M__ ♦
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  1. I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly.
  2. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega DNA aligner.

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega. Now, inIn my final step, I want to assess the per-residue read coverage of the consensus amino acid sequence to demonstrate an idea of confidence in that sequence.

Does anyone have any tips on how to go about doing this and whether there are existing tools for such things? I'd much prefer not to reinvent the wheel if I don't have to...

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega. Now, in my final step, I want to assess the per-residue read coverage of the consensus amino acid sequence to demonstrate an idea of confidence in that sequence.

Does anyone have any tips on how to go about doing this and whether there are existing tools for such things? I'd much prefer not to reinvent the wheel if I don't have to...

  1. I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly.
  2. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega DNA aligner.

In my final step, I want to assess the per-residue read coverage of the consensus amino acid sequence to demonstrate an idea of confidence in that sequence.

Does anyone have any tips on how to go about doing this and whether there are existing tools for such things?

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CephBirk
CephBirk
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RNASeq read coverage in protein space?

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega. Now, in my final step, I want to assess the per-residue read coverage of the consensus amino acid sequence to demonstrate an idea of confidence in that sequence.

Does anyone have any tips on how to go about doing this and whether there are existing tools for such things? I'd much prefer not to reinvent the wheel if I don't have to...