Computing Number Of Nucleotide And Genes On Each Chromosome
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8.6 years ago
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Hi!

I am interested in knowing number of nucleotides and genes on each chromosome for hg18 and hg19.

Any suggestions or links to get these numbers?

Thank you

chip-seq ucsc mysql • 3.2k views
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6
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8.6 years ago

Let's see if for once I can beat Pierre in posting a Mysql answer!! :-)

Remember that the human genome is not completely sequenced, as many repetitive and low complexity regions can not be sequenced with the current technologies. Moreover, hg18 and hg19 are the reference genomes, but it is likely that there is variability in the number of nucleotides between individuals.

Count the number of genes in hg18 and hg19, grouped by chromosome:

mysql -h genome-mysql.cse.ucsc.edu -u genome -D hg18 -N -A -e 'select chrom, count(*) from knownGene GROUP BY chrom'
mysql -h genome-mysql.cse.ucsc.edu -u genome -D hg19 -N -A -e 'select chrom, count(*) from knownGene GROUP BY chrom'

I recommend you to get the counts grouped by chromosomes, so you will be able to see which chromosomes you want to include.

For the number of nucleotides, maybe you can use the tool fetchChromSizes from the UCSC utils. http://hgdownload.cse.ucsc.edu/admin/exe/ , or use the chromInfo table:

mysql -h genome-mysql.cse.ucsc.edu -u genome -D hg18 -N -A -e 'select chrom,size from chromInfo'

However, this won't take into account centromers and regions with no coverage.

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That's not fair ! I was attending a meeting ! :-)

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7
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everything is fair in biostar and in bioinformatics :-)

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