text: user1075: I am working with two versions of the C. elegans genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in that region. For this, I need to know the correspondence between coordinates in genome 1 and coordinates in genome 2. I think a whole-genome alignment programme might help me, e. g. nucmer or mauve. I have run nucmer on the two genomes and got a delta file but I don't know how to interpret it. I have run show-coords on the delta file and obtained a .coords file. It seems more human-friendly. The first few lines look like this:
  /Users/user/Documents/project/output/genome/celegans/ref/wormbase/seq/c_elegans.PRJNA13758.WS245.genomic.fa /Users/user/Documents/project/output/genome/celegans/strain/seq/bristol/scaffolds.fa
  NUCMER
  
      [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [LEN R]  [LEN Q]  |  [COV R]  [COV Q]  | [TAGS]
  ===============================================================================================================================
         1      432  |      498      929  |      432      432  |   100.00  | 15072434 15371751  |     0.00     0.00  | I  I
         1      432  |     1002     1433  |      432      432  |   100.00  | 15072434 15371751  |     0.00     0.00  | I  I
  
  Does this mean that chromosome I starting at 1 and ending at 432 of version 1 corresponds to chromosome I starting at 498 and ending at 929 and that there is 100% identity between these two 432-long sequences? In this case, it's easy to find a correspondence between bases in version 1 and bases in version 2. However, some lines do not align sequences of the same length:
     1   237139  |     4022   241181  |   237139   237160  |    99.99  | 15072434 15371751  |     1.57     1.54  | I  I
  
  Also, in this sequence position 1 of chromosome I is aligned again? So is it aligning to more than one position in version 2 of the genome? Also one sequence is 237139 bases long and the other 237160 bases long. How do I know the internal structure?
  Can anybody guide me, please?
  I've also aligned the two genomes using Mauve:
  progressiveMauve c_elegans.PRJNA13758.WS245.genomic.fa scaffolds.fa --output scaffolds.mauve > scaffolds.txt
  
  I've tried to import the .mauve file into Python using Biopython but I got an error:
  alignment = SeqIO.read('scaffolds.mauve', "mauve")
  
  Traceback (most recent call last):
    File "code/mauve.py", line 4, in <module>
      alignment = SeqIO.read('scaffolds.mauve', "mauve")
    File "/Users/user/anaconda/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line 712, in read
      raise ValueError("More than one record found in handle")
  ValueError: More than one record found in handle
  
  Note that the alignment opened in the Mauve GUI looks fine. Unfortunately, the picture won't load here.
  I am working on Mac OSX.
  I would appreciate your help in understanding the delta file, resolving the Python error or any other support in finding a function between coordinates in version 1 of the genome and coordinates in version 2 of the genome.
  
  user77: A relatively convenient method would be to create a .chain file, as used by tools like liftOver and crossmap (and probably remap from NCBI). For your use-case, you can simply use the DoSameSpeciesLiftOver.pl command as described in the link. The resulting chain files are pretty self-explanatory and can be used to map BED files of regions of interest.
  
original_text: 1075: <p>I am working with two versions of the <em>C. elegans</em> genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in that region. For this, I need to know the correspondence between coordinates in genome 1 and coordinates in genome 2. I think a whole-genome alignment programme might help me, e. g. nucmer or mauve. I have run nucmer on the two genomes and got a delta file but I don't know how to interpret it. I have run <code>show-coords</code> on the delta file and obtained a .coords file. It seems more human-friendly. The first few lines look like this:</p>
  
  <pre><code>/Users/user/Documents/project/output/genome/celegans/ref/wormbase/seq/c_elegans.PRJNA13758.WS245.genomic.fa /Users/user/Documents/project/output/genome/celegans/strain/seq/bristol/scaffolds.fa
  NUCMER
  
      [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [LEN R]  [LEN Q]  |  [COV R]  [COV Q]  | [TAGS]
  ===============================================================================================================================
         1      432  |      498      929  |      432      432  |   100.00  | 15072434 15371751  |     0.00     0.00  | I  I
         1      432  |     1002     1433  |      432      432  |   100.00  | 15072434 15371751  |     0.00     0.00  | I  I
  </code></pre>
  
  <p>Does this mean that chromosome I starting at 1 and ending at 432 of version 1 corresponds to chromosome I starting at 498 and ending at 929 and that there is 100% identity between these two 432-long sequences? In this case, it's easy to find a correspondence between bases in version 1 and bases in version 2. However, some lines do not align sequences of the same length:</p>
  
  <pre><code>   1   237139  |     4022   241181  |   237139   237160  |    99.99  | 15072434 15371751  |     1.57     1.54  | I  I
  </code></pre>
  
  <p>Also, in this sequence position 1 of chromosome I is aligned again? So is it aligning to more than one position in version 2 of the genome? Also one sequence is 237139 bases long and the other 237160 bases long. How do I know the internal structure?</p>
  
  <p>Can anybody guide me, please?</p>
  
  <p>I've also aligned the two genomes using Mauve:</p>
  
  <pre><code>progressiveMauve c_elegans.PRJNA13758.WS245.genomic.fa scaffolds.fa --output scaffolds.mauve &gt; scaffolds.txt
  </code></pre>
  
  <p>I've tried to import the .mauve file into Python using Biopython but I got an error:</p>
  
  <pre><code>alignment = SeqIO.read('scaffolds.mauve', "mauve")
  
  Traceback (most recent call last):
    File "code/mauve.py", line 4, in &lt;module&gt;
      alignment = SeqIO.read('scaffolds.mauve', "mauve")
    File "/Users/user/anaconda/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line 712, in read
      raise ValueError("More than one record found in handle")
  ValueError: More than one record found in handle
  </code></pre>
  
  <p>Note that the alignment opened in the Mauve GUI looks fine. Unfortunately, the picture won't load here.</p>
  
  <p>I am working on Mac OSX.</p>
  
  <p>I would appreciate your help in understanding the delta file, resolving the Python error or any other support in finding a function between coordinates in version 1 of the genome and coordinates in version 2 of the genome.</p>
   77: <p>A relatively convenient method would be to create a .chain file, as used by tools like <code>liftOver</code> and <code>crossmap</code> (and probably remap from NCBI). For your use-case, you can simply use the <a href="http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl" rel="nofollow noreferrer">DoSameSpeciesLiftOver.pl</a> command as described in the link. The resulting chain files are pretty self-explanatory and can be used to map BED files of regions of interest.</p>
  