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Chromosomal Gene Density Calculation And Visualization

I am looking for a tool/package/script that would be able to calculate chromosomal region gene density and maybe visualize it.

TIA

human chromosome gene
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updated by Casey Bergman Casey Bergman • written by Paulo Nuin Paulo Nuin

Yep, but the visualization part here is secondary, the gene density per region is the main question.

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written by Paulo Nuin Paulo Nuin

OK, Paulo I will remove the visualization tag.

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written by Khader Shameer Khader Shameer

Let's make a code-golf out of this. Can you define a format how chrom. regions are defined.

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written by Michael Dondrup Michael Dondrup

2 answers

Something like this, using mysql 'group by' ?

> mysql -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg18 -e 'select chrom,1000000*ceil(txStart/1000000) as 'start', count(*) from knownGene group by 1,2' 
chrom   start   count(*)
chr1    1000000 88
chr1    2000000 180
chr1    3000000 48
chr1    4000000 38
chr1    5000000 6
chr1    6000000 8
chr1    7000000 74
chr1    8000000 21
chr1    9000000 19
(...)
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Can you explain the 1000000*ceil(txStart/1000000) part of the query?

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written by Paulo Nuin Paulo Nuin

it's just for "binning' the genome with a window of 1000000pb. I group the transcription start in the same window by dividing it by the window size.

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written by Pierre Lindenbaum Pierre Lindenbaum

The only thing here is that I get more than 60000 genes.

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written by Paulo Nuin Paulo Nuin

If your organism is in the UCSC Genome database, try GenomeGraphs for visualization:

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updated by Ram Ram • written by Casey Bergman Casey Bergman

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