size of the exome per each chromosome of hg38

[Bogdan Tanasa]

Dear all,

please could you advise, what is the easiest way to obtain the size of the exome per each chromosome of hg38 ?

many thanks,

-- bogdan

[Christopher Lee]

Hi Bogdan,

Thank you for your question about the obtaining the exome size per
chromosome of the hg38 Human assembly. The fastest method for
obtaining this information for a wide range of organisms and gene
tracks is to:

1. Download the featureBits program appropriate for your operating
system from our directory of utilities:
http://hgdownload.soe.ucsc.edu/admin/exe/

2. Set up an .hg.conf file (note the leading ".") in your home
directory according to the "Using the MySQL server with our utilities"
section of the following page:
http://genome.ucsc.edu/goldenPath/help/mysql.html

3. Use the following command to get base pairs/genome:
for chrom in {1..22} X Y M; do echo chr$chrom; featureBits
-chrom=chr$chrom hg38 knownGene; done

You can change the table, knownGene in this case, to refGene,
wgEncodeGencodeCompV24, etc, in order to obtain different gene
prediction program exon sizes, or you can change the database name to
obtain exon statistics for another organism. Running this command will
create output like the following:
chr1
11211593 bases of 230486321 (4.864%) in intersection
chr2
8527909 bases of 240551141 (3.545%) in intersection
chr3
6774604 bases of 198100344 (3.420%) in intersection

where the first number is the size in base pairs of all the exons on
that chromosome.

I hope this is helpful, please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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