Body: <p>Currently I'm trying to perform whole mtDNA sequencing and mapping to reference genome to extract variants.</p>
  <p>To minimise the nuMT (nuclear mt DNA segment), I'm going to use the hg19 human genome as a reference. In the analysis, I should provide nuclear fasta and mt fasta. In this case, Could I concatenate the fasta of Chr.1-22, X, Y (NC_000001.10-NC_000024.9) to provide a reference fasta?</p>
  <p>This is the first time I have analyzed the human genome.</p>
  <p>Best regards,</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-07T19:57:40.150Z
Comments.Text: This post needs more information. Could you please explain what your input files are, what program you are using for the mapping, and why you need whole nuclear chromosomes for mapping to the mitochondrial genome?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-08T03:04:58.990Z
Comments.Text: Yes you can concat mtDNA sequence with human chromosomes if it's not in the genome file. However, you need to understand the behavior of your aligner and order of your chromosomes in the fasta file. Sometimes people align the reads to nuclear genome first and align the unaligned reads to mito genome etc. This is tricky because of nuclear mt DNA segment. I suggest read publications on the topic and take the best action depending on your goal.  It's an active research area.
Comments.UserDisplayName: Supertech
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-08T20:48:22.267Z
Comments.Text: What do you mean by the word "minimize"?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-09T15:46:59.677Z
Comments.Text: My suggestion is that you simply map against the full human reference (containing all autosomes, sex chromosomes and mtdna). This will capture numtDNA to the corresponding autosomes and produce cleaner mt alignments. Only then you extract and work with the mt alignment. Mind that you have to use after this a variant caller that is aware you are working with haploid data. do you work with rCRS, or the one 2bp longer? or either is fine?
Comments.UserDisplayName: JRodrigoF
Tags: <genome><human><hg19>
Title: How should I prepare human genome reference file?
ThreadText: # How should I prepare human genome reference file?
  
  (Asked by: username_0 on 2024-05-06)
  
  Currently I'm trying to perform whole mtDNA sequencing and mapping to reference genome to extract variants.
  
  To minimise the nuMT (nuclear mt DNA segment), I'm going to use the hg19 human genome as a reference. In the analysis, I should provide nuclear fasta and mt fasta. In this case, Could I concatenate the fasta of Chr.1-22, X, Y (NC\_000001.10-NC\_000024.9) to provide a reference fasta?
  
  This is the first time I have analyzed the human genome.
  
  Best regards,
  
  **Tags:** genome, human, hg19
  
  > **Comments:**
  > **username_1**: This post needs more information. Could you please explain what your input files are, what program you are using for the mapping, and why you need whole nuclear chromosomes for mapping to the mitochondrial genome?  
  > **username_2**: Yes you can concat mtDNA sequence with human chromosomes if it's not in the genome file. However, you need to understand the behavior of your aligner and order of your chromosomes in the fasta file. Sometimes people align the reads to nuclear genome first and align the unaligned reads to mito genome etc. This is tricky because of nuclear mt DNA segment. I suggest read publications on the topic and take the best action depending on your goal.  It's an active research area.  
  > **username_3**: What do you mean by the word "minimize"?  
  > **username_4**: My suggestion is that you simply map against the full human reference (containing all autosomes, sex chromosomes and mtdna). This will capture numtDNA to the corresponding autosomes and produce cleaner mt alignments. Only then you extract and work with the mt alignment. Mind that you have to use after this a variant caller that is aware you are working with haploid data. do you work with rCRS, or the one 2bp longer? or either is fine?  
  
  ---
  
  ## 0 answers
  
  