Answers.Body: <p>I will try to answer the different questions.</p>
  <ol>
  <li>Do you mean aligning the original DNA fragments from a sample to the consensus obtained from the same sample? It makes sense for a few reasons i) authentication, you can measure the damage patterns ii) you can check that the consensus is correct.</li>
  <li>Most people simply align to the rCRS and call the consensus there.</li>
  <li>I recommend endoCaller from schmutzi (<a href="https://github.com/grenaud/schmutzi/blob/master/src/endoCaller.cpp" rel="nofollow noreferrer">https://github.com/grenaud/schmutzi/blob/master/src/endoCaller.cpp</a>). It is designed for calling consensus for mitochondria even in the presence of damage. To evaluate damage patterns, I recommend this small program: <a href="https://github.com/grenaud/bam2prof" rel="nofollow noreferrer">https://github.com/grenaud/bam2prof</a></li>
  </ol>
  <p>I hope this answers it.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-03T12:22:08.867Z
Answers.LastActivityDate: 2024-04-03T12:22:08.867Z
Answers.UserDisplayName: Gabriel Renaud
Body: <p>I have some doubts in how to proceed to compare ancient mtDNA with modern mtDNA. A little more context:</p>
  <p><strong>The problem:</strong></p>
  <p>I have some FASTQs associated with a given FASTA. They contain mtDNA. My goal is to extract the mtDNA from those FASTQs and compare with a reference mtDNA to calculate the average and SD of that difference.
  I currently download the samples FASTA and FASTQs from AMTDB (<a href="https://amtdb.org/samples" rel="nofollow noreferrer">https://amtdb.org/samples</a>).
  My final goal is to compare ancient mtDNA with modern mtDNA to analyze the deterioration based on the degradation patterns.</p>
  <p><strong>What I'm lacking in knowledge:</strong></p>
  <ol>
  <li><p>Does it make sense if I align the FASTQ with the corresponded downloaded FASTA? I mean, if the FASTA was already generated with those reads, wouldn't that be redundant?</p>
  </li>
  <li><p>Could I use an arbitrary mtDNA FASTA to align and compare? That would assume mtDNA in humans is very similar (I have doubts if that would be a safe assumption, since my goal is to compare those ancient samples with a modern and not damaged sample)</p>
  </li>
  <li><p>In any case, is there a recommended program to compare the results of the processing of the FASTQs with the reference FASTA?</p>
  </li>
  </ol>
  <p>Thank you for your help.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-11T13:09:01.103Z
Comments.Text: Can you please [edit] your question and explain the relationship between these fastqs and fasta files you mention? You should probably also tell us what species you are working with, should we assume human?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-11T13:14:18.040Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-05T04:07:03.407Z
Comments.Text: The question is a project and better split into individual parts. Is this metagenomics data? It appears to be, but without knowing that can't help.
Comments.UserDisplayName: M__
Tags: <fasta><fastq><mtdna>
Title: Compare FASTQ reconstructions to mtDNA
ThreadText: # Compare FASTQ reconstructions to mtDNA
  
  (Asked by: username_0 on 2024-03-11)
  
  I have some doubts in how to proceed to compare ancient mtDNA with modern mtDNA. A little more context:
  
  **The problem:**
  
  I have some FASTQs associated with a given FASTA. They contain mtDNA. My goal is to extract the mtDNA from those FASTQs and compare with a reference mtDNA to calculate the average and SD of that difference.
  I currently download the samples FASTA and FASTQs from AMTDB (<https://amtdb.org/samples>).
  My final goal is to compare ancient mtDNA with modern mtDNA to analyze the deterioration based on the degradation patterns.
  
  **What I'm lacking in knowledge:**
  
  1. Does it make sense if I align the FASTQ with the corresponded downloaded FASTA? I mean, if the FASTA was already generated with those reads, wouldn't that be redundant?
  2. Could I use an arbitrary mtDNA FASTA to align and compare? That would assume mtDNA in humans is very similar (I have doubts if that would be a safe assumption, since my goal is to compare those ancient samples with a modern and not damaged sample)
  3. In any case, is there a recommended program to compare the results of the processing of the FASTQs with the reference FASTA?
  
  Thank you for your help.
  
  **Tags:** fasta, fastq, mtdna
  
  > **Comments:**
  > **username_1**: Can you please [edit] your question and explain the relationship between these fastqs and fasta files you mention? You should probably also tell us what species you are working with, should we assume human?  
  > **username_2**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_3**: The question is a project and better split into individual parts. Is this metagenomics data? It appears to be, but without knowing that can't help.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2024-04-03. Score: 2 | Accepted answer
  
  I will try to answer the different questions.
  
  1. Do you mean aligning the original DNA fragments from a sample to the consensus obtained from the same sample? It makes sense for a few reasons i) authentication, you can measure the damage patterns ii) you can check that the consensus is correct.
  2. Most people simply align to the rCRS and call the consensus there.
  3. I recommend endoCaller from schmutzi (<https://github.com/grenaud/schmutzi/blob/master/src/endoCaller.cpp>). It is designed for calling consensus for mitochondria even in the presence of damage. To evaluate damage patterns, I recommend this small program: <https://github.com/grenaud/bam2prof>
  
  I hope this answers it.
  
  
  ---
  
  