Answers.Body: <p>The chromosome sizes can be retrieved with (to use for sanity check):</p>
  <pre><code>&gt; ./faSize -veryDetailed -tab hs37d5.fa.gz
  1   249250621   23970000    225280621   225280621   0
  2   243199373   4994855 238204518   238204518   0
  3   198022430   3225295 194797135   194797135   0
  4   191154276   3492600 187661676   187661676   0
  ...
  </code></pre>
  <p>(first column is chromosome ID, second column is chromosome size).</p>
  <p>Afterwards, the centromere coordinates are retrieved through (in this case I used hg19 since I'm working with <code>hs37d5</code>):</p>
  <pre><code>&gt; curl -s &quot;http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz&quot; \
    | gunzip -c | grep acen | sed 's/chr//g' | sort -n &gt; hg19.centromeres
  </code></pre>
  <p>The coordinates for each chromosome arm can be computed from the chromosome size and centromere coordinates.</p>
  <p>N.B. As per <a href="http://genome.ucsc.edu/FAQ/FAQtracks#tracks1" rel="nofollow noreferrer">UCSC documentation</a>, cytoband's start is 0-based, while end is 1-based.
  As a sanity check you might want to compare the end of the last cytoband for each chromosome, with the chromosome size (they should be the same, since end is 1-based).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-04-29T22:43:33.820Z
Answers.LastActivityDate: 2022-04-29T22:43:33.820Z
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Body: <p>I would like to get chromosome arms' coordinates for genome reference <code>hs37d5</code> (<a href="ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/" rel="nofollow noreferrer">ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/</a>), but I could not find them either online, or the directory listed above.</p>
  <p>Is there a way to extract such coordinates from one of the available files (e.g., from the fasta)?</p>
  
Tags: <reference-genome><chromosomes>
Title: Extract chromosome arms' coordinates for specific reference
ThreadText: # Extract chromosome arms' coordinates for specific reference
  
  (Asked by: username_0 on 2022-04-29)
  
  I would like to get chromosome arms' coordinates for genome reference `hs37d5` (<ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/>), but I could not find them either online, or the directory listed above.
  
  Is there a way to extract such coordinates from one of the available files (e.g., from the fasta)?
  
  **Tags:** reference-genome, chromosomes
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2022-04-29. Score: 1 | Accepted answer
  
  The chromosome sizes can be retrieved with (to use for sanity check):
  
  ```
  > ./faSize -veryDetailed -tab hs37d5.fa.gz
  1   249250621   23970000    225280621   225280621   0
  2   243199373   4994855 238204518   238204518   0
  3   198022430   3225295 194797135   194797135   0
  4   191154276   3492600 187661676   187661676   0
  ...
  
  ```
  
  (first column is chromosome ID, second column is chromosome size).
  
  Afterwards, the centromere coordinates are retrieved through (in this case I used hg19 since I'm working with `hs37d5`):
  
  ```
  > curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz" \
    | gunzip -c | grep acen | sed 's/chr//g' | sort -n > hg19.centromeres
  
  ```
  
  The coordinates for each chromosome arm can be computed from the chromosome size and centromere coordinates.
  
  N.B. As per [UCSC documentation](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1), cytoband's start is 0-based, while end is 1-based.
  As a sanity check you might want to compare the end of the last cytoband for each chromosome, with the chromosome size (they should be the same, since end is 1-based).
  
  
  ---
  
  