<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>

CC BY-SA 4.0
2022-04-29T22:43:33.820Z
2022-04-29T22:43:33.820Z
gc5
<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>

<reference-genome><chromosomes>
Extract chromosome arms' coordinates for specific reference
# 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

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## 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, 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).


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