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Old 10-01-2010, 09:14 AM   #1
yuanzhi
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Default how many bases are in UCSC hg18?

Hi, all

Anyone knows where I can find the total size of UCSC hg18?

Thanks
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Old 10-01-2010, 09:18 AM   #2
kmcarr
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Quote:
Originally Posted by yuanzhi View Post
Anyone knows where I can find the total size of UCSC hg18?
On the hg18 information page at UCSC.
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Old 10-01-2010, 09:22 AM   #3
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awesome, thanks a lot!
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Old 11-15-2010, 06:09 AM   #4
yuanzhi
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hi, I just noticed that the total size of hg18 (3.1billion bases) includes gaps. Does anyone know the total size of hg18 excluding gaps?

Thanks in advance
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Old 11-15-2010, 07:49 AM   #5
bioinfosm
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It was right there:
http://genome.ucsc.edu/goldenPath/stats.html#hg18
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Old 11-15-2010, 07:58 AM   #6
yuanzhi
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Great. Thanks a lot!!

It is amazing that UCSC has all the statistics. I was trying to search them in UCSC and couldn't find them... I probably should spend more time in studying UCSC..

One more silly question: do you know the difference between Assembled Size and Sequenced Size?

I am trying to count the percent of base mapped to the whole genome and am not sure which size I should use..
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Old 11-16-2010, 01:03 AM   #7
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I believe assembled size includes the size of known gaps in the genome assembly. The sequenced size does not include the size of these gaps. Using physical mapping of a genome (e.g. BAC library fingerprinting or end sequencing) it may be possible to tell the size of a partially sequenced section of the genome during the assembly process, while the entire sequence may not actually be sequenced yet. Nature published a discussion of Gaps in the Human Genome.

Since there are regions of the genome that are difficult to sequence and assemble with existing technology (e.g. heterochromatin), the difference between assembled and sequenced genome size is likely to persist...
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Old 11-16-2010, 01:41 PM   #8
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I agree with the sequenced and assembled size, and would guess using sequenced size makes sense. Because the gaps are not even checked if you are mapping to a reference..
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